diff --git a/Snakefile b/Snakefile
index 48e0b619aeb6af55910bb0f6b86285027b952403..eef73fa9676aad5a24bca5d1ca137e80dff00682 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1,12 +1,9 @@
"""General purpose RNA-Seq analysis pipeline developed by the Zavolan Lab"""
-
import os
-import sys
-
import pandas as pd
import shutil
-import glob
-from zipfile import ZipFile
+workdir: config['workdir']
+
# Get sample table
samples_table = pd.read_csv(
@@ -19,8 +16,7 @@ samples_table = pd.read_csv(
)
# Global config
-localrules: finish, rename_star_rpm_for_alfa, prepare_files_for_report, \
- prepare_MultiQC_config
+localrules: start, finish, rename_star_rpm_for_alfa, prepare_multiqc_config
# Create log directories
os.makedirs(
@@ -47,11 +43,97 @@ rule finish:
Rule for collecting outputs
"""
input:
- MultiQC_report = expand(
+ multiqc_report = os.path.join(
+ config['output_dir'],
+ "multiqc_summary"),
+ bigWig = expand(
+ os.path.join(
+ config["output_dir"],
+ "samples",
+ "{sample}",
+ "bigWig",
+ "{unique_type}",
+ "{sample}_{unique_type}_{strand}.bw"),
+ sample=samples_table.index.values,
+ strand=["plus", "minus"],
+ unique_type=["Unique", "UniqueMultiple"])
+
+
+rule start:
+ '''
+ Get samples
+ '''
+ input:
+ reads = lambda wildcards:
+ samples_table.loc[wildcards.sample, wildcards.mate],
+
+ output:
+ reads = os.path.join(
+ config["output_dir"],
+ "samples",
+ "{sample}",
+ "start",
+ "{sample}.{mate}.fastq.gz")
+
+ log:
+ stderr = os.path.join(
+ config["log_dir"],
+ "samples",
+ "{sample}",
+ "start_{sample}.{mate}.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "samples",
+ "{sample}",
+ "start_{sample}.{mate}.stdout.log")
+
+ shell:
+ "(cp {input.reads} {output.reads}) \
+ 1> {log.stdout} 2> {log.stderr} "
+
+
+rule fastqc:
+ '''
+ A quality control tool for high throughput sequence data
+ '''
+ input:
+ reads = os.path.join(
+ config["output_dir"],
+ "samples",
+ "{sample}",
+ "start",
+ "{sample}.{mate}.fastq.gz")
+
+ output:
+ outdir = directory(
os.path.join(
- config['output_dir'],
- "multiqc_summary"),
- output_dir=config["output_dir"])
+ config["output_dir"],
+ "samples",
+ "{sample}",
+ "fastqc",
+ "{mate}"))
+
+ threads: 2
+
+ singularity:
+ "docker://zavolab/fastqc:0.11.9-slim"
+
+ log:
+ stderr = os.path.join(
+ config["log_dir"],
+ "samples",
+ "{sample}",
+ "fastqc_{mate}.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "samples",
+ "{sample}",
+ "fastqc_{mate}.stdout.log")
+
+ shell:
+ "(mkdir -p {output.outdir}; \
+ fastqc --outdir {output.outdir} {input.reads}) \
+ 1> {log.stdout} 2> {log.stderr}"
rule create_index_star:
@@ -121,25 +203,25 @@ rule create_index_star:
--sjdbGTFfile {input.gtf}) \
1> {log.stdout} 2> {log.stderr}"
-
rule extract_transcriptome:
- """ Create transcriptome from genome and gene annotations """
+ """
+ Create transcriptome from genome and gene annotations
+ """
input:
genome = lambda wildcards:
samples_table['genome'][
- samples_table['organism'] == wildcards.organism
- ][0],
+ samples_table['organism'] == wildcards.organism][0],
gtf = lambda wildcards:
samples_table['gtf'][
- samples_table['organism'] == wildcards.organism
- ][0]
+ samples_table['organism'] == wildcards.organism][0]
+
output:
transcriptome = os.path.join(
- config['output_dir'],
- "transcriptome",
- "{organism}",
- "transcriptome.fa",
- )
+ config['output_dir'],
+ "transcriptome",
+ "{organism}",
+ "transcriptome.fa")
+
log:
stderr = os.path.join(
config['log_dir'],
@@ -147,8 +229,10 @@ rule extract_transcriptome:
stdout = os.path.join(
config['log_dir'],
"{organism}_extract_transcriptome.log")
+
singularity:
"docker://zavolab/gffread:0.11.7-slim"
+
shell:
"(gffread \
-w {output.transcriptome} \
@@ -156,102 +240,17 @@ rule extract_transcriptome:
1> {log.stdout} 2> {log.stderr}"
-rule extract_decoys_salmon:
- """
- Extract names of the genome targets
- """
- input:
- genome = lambda wildcards:
- samples_table['genome']
- [samples_table['organism'] == wildcards.organism]
- [0],
-
- output:
- decoys = os.path.join(
- config['output_dir'],
- "transcriptome",
- "{organism}",
- "decoys.txt")
-
- singularity:
- "docker://bash:5.0.16"
-
- log:
- stderr = os.path.join(
- config['log_dir'],
- "{organism}_extract_decoys_salmon.stderr.log"),
- stdout = os.path.join(
- config['log_dir'],
- "{organism}_extract_decoys_salmon.stdout.log")
-
- threads: 1
-
- shell:
- """
- (grep "^>" <{input.genome} \
- | cut -d " " -f 1 > {output.decoys} && \
- sed -i.bak -e 's/>//g' {output.decoys}) \
- 1> {log.stdout} 2> {log.stderr}
- """
-
-
-rule concatenate_transcriptome_and_genome:
- """
- Concatenate genome and transcriptome
- """
- input:
- transcriptome = os.path.join(
- config['output_dir'],
- "transcriptome",
- "{organism}",
- "transcriptome.fa",
- ),
- genome = lambda wildcards:
- samples_table['genome']
- [samples_table['organism'] == wildcards.organism]
- [0],
-
- output:
- genome_transcriptome = os.path.join(
- config['output_dir'],
- "transcriptome",
- "{organism}",
- "genome_transcriptome.fa",
- )
-
- singularity:
- "docker://bash:5.0.16"
-
- log:
- stderr = os.path.join(
- config['log_dir'],
- "{organism}_concatenate_transcriptome_and_genome.stderr.log"),
- stdout = os.path.join(
- config['log_dir'],
- "{organism}_concatenate_transcriptome_and_genome.stdout.log")
-
- shell:
- "(cat {input.transcriptome} {input.genome} \
- 1> {output.genome_transcriptome}) \
- 1> {log.stdout} 2> {log.stderr}"
-
-
rule create_index_salmon:
"""
Create index for Salmon quantification
"""
input:
- genome_transcriptome = os.path.join(
- config['output_dir'],
- "transcriptome",
- "{organism}",
- "genome_transcriptome.fa",
- ),
- decoys = os.path.join(
- config['output_dir'],
- "transcriptome",
- "{organism}",
- "decoys.txt")
+ transcriptome = os.path.join(
+ config['output_dir'],
+ "transcriptome",
+ "{organism}",
+ "transcriptome.fa")
+
output:
index = directory(
os.path.join(
@@ -278,8 +277,7 @@ rule create_index_salmon:
shell:
"(salmon index \
- --transcripts {input.genome_transcriptome} \
- --decoys {input.decoys} \
+ --transcripts {input.transcriptome} \
--index {output.index} \
--kmerLen {params.kmerLen} \
--threads {threads}) \
@@ -292,11 +290,11 @@ rule create_index_kallisto:
"""
input:
transcriptome = os.path.join(
- config['output_dir'],
- "transcriptome",
- "{organism}",
- "transcriptome.fa",
- )
+ config['output_dir'],
+ "transcriptome",
+ "{organism}",
+ "transcriptome.fa")
+
output:
index = os.path.join(
config['kallisto_indexes'],
@@ -332,8 +330,7 @@ rule extract_transcripts_as_bed12:
"""
input:
gtf = lambda wildcards:
- samples_table['gtf']
- [0]
+ samples_table['gtf'][0]
output:
bed12 = os.path.join(
@@ -364,18 +361,17 @@ rule index_genomic_alignment_samtools:
input:
bam = os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
"map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam")
-
+ "{sample}.{seqmode}.Aligned.sortedByCoord.out.bam"),
output:
bai = os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
"map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam.bai")
+ "{sample}.{seqmode}.Aligned.sortedByCoord.out.bam.bai")
singularity:
"docker://zavolab/samtools:1.10-slim"
@@ -385,14 +381,14 @@ rule index_genomic_alignment_samtools:
log:
stderr = os.path.join(
config["log_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
- "index_genomic_alignment_samtools.stderr.log"),
+ "index_genomic_alignment_samtools.{seqmode}.stderr.log"),
stdout = os.path.join(
config["log_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
- "index_genomic_alignment_samtools.stdout.log")
+ "index_genomic_alignment_samtools.{seqmode}.stdout.log")
shell:
"(samtools index {input.bam} {output.bai};) \
@@ -400,120 +396,132 @@ rule index_genomic_alignment_samtools:
rule star_rpm:
- ''' Create stranded bedgraph coverage with STARs RPM normalisation '''
- input:
- bam = os.path.join(
- config["output_dir"],
- "{seqmode}",
- "{sample}",
- "map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam"),
- bai = os.path.join(
- config["output_dir"],
- "{seqmode}",
- "{sample}",
- "map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam.bai")
+ '''
+ Create stranded bedgraph coverage with STARs RPM normalisation
+ '''
+ input:
+ bam = lambda wildcards:
+ expand(
+ os.path.join(
+ config["output_dir"],
+ "samples",
+ "{sample}",
+ "map_genome",
+ "{sample}.{seqmode}.Aligned.sortedByCoord.out.bam"),
+ sample=wildcards.sample,
+ seqmode=samples_table.loc[wildcards.sample, 'seqmode']),
+ bai = lambda wildcards:
+ expand(
+ os.path.join(
+ config["output_dir"],
+ "samples",
+ "{sample}",
+ "map_genome",
+ "{sample}.{seqmode}.Aligned.sortedByCoord.out.bam.bai"),
+ sample=wildcards.sample,
+ seqmode=samples_table.loc[wildcards.sample, 'seqmode']),
output:
- str1 = (os.path.join(
+ str1 = os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
"STAR_coverage",
"{sample}_Signal.Unique.str1.out.bg"),
- os.path.join(
+ str2 = os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
"STAR_coverage",
- "{sample}_Signal.UniqueMultiple.str1.out.bg")),
- str2 = (os.path.join(
+ "{sample}_Signal.UniqueMultiple.str1.out.bg"),
+ str3 = os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
"STAR_coverage",
"{sample}_Signal.Unique.str2.out.bg"),
- os.path.join(
+ str4 = os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
"STAR_coverage",
- "{sample}_Signal.UniqueMultiple.str2.out.bg"))
+ "{sample}_Signal.UniqueMultiple.str2.out.bg")
params:
- out_dir = lambda wildcards, output: os.path.dirname(output.str1[0]),
- prefix = lambda wildcards, output: os.path.join(os.path.dirname(output.str1[0]),
- str(wildcards.sample) + "_"),
+ out_dir = lambda wildcards, output:
+ os.path.dirname(output.str1),
+ prefix = lambda wildcards, output:
+ os.path.join(
+ os.path.dirname(output.str1),
+ str(wildcards.sample) + "_"),
stranded = "Stranded"
singularity:
"docker://zavolab/star:2.7.3a-slim"
- log:
+ log:
stderr = os.path.join(
config["log_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
- "star_rpm_single_end.stderr.log"),
+ "star_rpm.stderr.log"),
stdout = os.path.join(
config["log_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
- "star_rpm_single_end.stdout.log")
+ "star_rpm.stdout.log")
threads: 4
shell:
- """
- (mkdir -p {params.out_dir}; \
+ "(mkdir -p {params.out_dir}; \
chmod -R 777 {params.out_dir}; \
STAR \
--runMode inputAlignmentsFromBAM \
--runThreadN {threads} \
--inputBAMfile {input.bam} \
- --outWigType "bedGraph" \
+ --outWigType \"bedGraph\" \
--outWigStrand {params.stranded} \
- --outWigNorm "RPM" \
+ --outWigNorm \"RPM\" \
--outFileNamePrefix {params.prefix}) \
- 1> {log.stdout} 2> {log.stderr}
- """
+ 1> {log.stdout} 2> {log.stderr}"
rule rename_star_rpm_for_alfa:
input:
str1 = os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
"STAR_coverage",
"{sample}_Signal.{unique}.str1.out.bg"),
str2 = os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
"STAR_coverage",
"{sample}_Signal.{unique}.str2.out.bg")
-
+
output:
plus = os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
"ALFA",
"{unique}",
"{sample}_Signal.{unique}.out.plus.bg"),
minus = os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
"ALFA",
"{unique}",
"{sample}_Signal.{unique}.out.minus.bg")
-
+
params:
- orientation = lambda wildcards: samples_table.loc[wildcards.sample, "kallisto_directionality"]
-
+ orientation = lambda wildcards:
+ samples_table.loc[wildcards.sample, "kallisto_directionality"]
+
run:
if params['orientation'] == "--fr":
shutil.copy2(input['str1'], output['plus'])
@@ -525,21 +533,29 @@ rule rename_star_rpm_for_alfa:
rule calculate_TIN_scores:
"""
- Caluclate transcript integrity (TIN) score
+ Calculate transcript integrity (TIN) score
"""
input:
- bam = os.path.join(
- config['output_dir'],
- "{seqmode}",
- "{sample}",
- "map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam"),
- bai = os.path.join(
- config['output_dir'],
- "{seqmode}",
- "{sample}",
- "map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam.bai"),
+ bam = lambda wildcards:
+ expand(
+ os.path.join(
+ config['output_dir'],
+ "samples",
+ "{sample}",
+ "map_genome",
+ "{sample}.{seqmode}.Aligned.sortedByCoord.out.bam"),
+ sample=wildcards.sample,
+ seqmode=samples_table.loc[wildcards.sample, 'seqmode']),
+ bai = lambda wildcards:
+ expand(
+ os.path.join(
+ config['output_dir'],
+ "samples",
+ "{sample}",
+ "map_genome",
+ "{sample}.{seqmode}.Aligned.sortedByCoord.out.bam.bai"),
+ sample=wildcards.sample,
+ seqmode=samples_table.loc[wildcards.sample, 'seqmode']),
transcripts_bed12 = os.path.join(
config['output_dir'],
"full_transcripts_protein_coding.bed")
@@ -547,7 +563,7 @@ rule calculate_TIN_scores:
output:
TIN_score = os.path.join(
config['output_dir'],
- "{seqmode}",
+ "samples",
"{sample}",
"TIN",
"TIN_score.tsv")
@@ -558,9 +574,7 @@ rule calculate_TIN_scores:
log:
stderr = os.path.join(
config['log_dir'],
- "{seqmode}",
- "{sample}",
- "calculate_TIN_scores.log")
+ "{sample}_calculate_TIN_scores.log")
threads: 8
@@ -584,25 +598,30 @@ rule merge_TIN_scores:
TIN_score = expand(
os.path.join(
config['output_dir'],
- "{seqmode}",
+ "samples",
"{sample}",
"TIN",
"TIN_score.tsv"),
- zip,
- sample=[i for i in list(samples_table.index.values)],
- seqmode=[samples_table.loc[i, 'seqmode']
- for i in list(samples_table.index.values)])
+ sample=samples_table.index.values),
output:
TIN_scores_merged = os.path.join(
config['output_dir'],
"TIN_scores_merged.tsv")
+ log:
+ stderr = os.path.join(
+ config['log_dir'],
+ "merge_TIN_scores.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "merge_TIN_scores.stdout.log")
+
params:
TIN_score_merged_paths = ",".join(expand(
os.path.join(
config['output_dir'],
- "{seqmode}",
+ "samples",
"{sample}",
"TIN",
"TIN_score.tsv"),
@@ -611,14 +630,6 @@ rule merge_TIN_scores:
seqmode=[samples_table.loc[i, 'seqmode']
for i in list(samples_table.index.values)]))
- log:
- stderr = os.path.join(
- config['log_dir'],
- "merge_TIN_scores.stderr.log"),
- stdout = os.path.join(
- config["log_dir"],
- "merge_TIN_scores.stdout.log")
-
threads: 1
singularity:
@@ -681,13 +692,14 @@ rule salmon_quantmerge_genes:
salmon_in = expand(
os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
- "salmon_quant",
- "quant.genes.sf"),
+ "{sample}.salmon.{seqmode}",
+ "quant.sf"),
zip,
- sample=list(samples_table.index.values),
- seqmode=list(samples_table["seqmode"]))
+ sample=samples_table.index.values,
+ seqmode=[samples_table.loc[i, 'seqmode']
+ for i in list(samples_table.index.values)])
output:
salmon_out = os.path.join(
@@ -697,15 +709,16 @@ rule salmon_quantmerge_genes:
"genes_{salmon_merge_on}.tsv")
params:
- salmon_dir = expand(
+ salmon_in = expand(
os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
- "salmon_quant"),
+ "{sample}.salmon.{seqmode}"),
zip,
- sample=list(samples_table.index.values),
- seqmode=list(samples_table["seqmode"])),
+ sample=[i for i in list(samples_table.index.values)],
+ seqmode=[samples_table.loc[i, 'seqmode']
+ for i in list(samples_table.index.values)]),
sample_name_list = expand(
"{sample}",
sample=list(samples_table.index.values)),
@@ -726,7 +739,7 @@ rule salmon_quantmerge_genes:
shell:
"(salmon quantmerge \
- --quants {params.salmon_dir} \
+ --quants {params.salmon_in} \
--genes \
--names {params.sample_name_list} \
--column {params.salmon_merge_on} \
@@ -742,13 +755,14 @@ rule salmon_quantmerge_transcripts:
salmon_in = expand(
os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
- "salmon_quant",
+ "{sample}.salmon.{seqmode}",
"quant.sf"),
zip,
- sample=list(samples_table.index.values),
- seqmode=list(samples_table["seqmode"])),
+ sample=[i for i in list(samples_table.index.values)],
+ seqmode=[samples_table.loc[i, 'seqmode']
+ for i in list(samples_table.index.values)])
output:
salmon_out = os.path.join(
@@ -758,15 +772,17 @@ rule salmon_quantmerge_transcripts:
"transcripts_{salmon_merge_on}.tsv")
params:
- salmon_dir = expand(
+ salmon_in = expand(
os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
- "salmon_quant"),
+ "{sample}.salmon.{seqmode}"),
zip,
- sample=list(samples_table.index.values),
- seqmode=list(samples_table["seqmode"])),
+ sample=[i for i in list(samples_table.index.values)],
+ seqmode=[samples_table.loc[i, 'seqmode']
+ for i in list(samples_table.index.values)]),
+
sample_name_list = expand(
"{sample}",
sample=list(samples_table.index.values)),
@@ -787,24 +803,23 @@ rule salmon_quantmerge_transcripts:
shell:
"(salmon quantmerge \
- --quants {params.salmon_dir} \
+ --quants {params.salmon_in} \
--names {params.sample_name_list} \
--column {params.salmon_merge_on} \
--output {output.salmon_out}) \
1> {log.stdout} 2> {log.stderr}"
-#################################################################################
-### ALFA: Annotation Landscape For Aligned reads
-#################################################################################
-
+# ALFA: Annotation Landscape For Aligned reads
directionality = {"--fr": "fr-firststrand", "--rf": "fr-secondstrand"}
rule generate_alfa_index:
''' Generate ALFA index files from sorted GTF file '''
input:
- gtf = lambda wildcards: samples_table["gtf"][samples_table["organism"]==wildcards.organism][0],
+ gtf = lambda wildcards:
+ samples_table["gtf"]
+ [samples_table["organism"] == wildcards.organism][0],
chr_len = os.path.join(
config["star_indexes"],
"{organism}",
@@ -813,124 +828,141 @@ rule generate_alfa_index:
"chrNameLength.txt"),
output:
- index_stranded = os.path.join(config["alfa_indexes"],
- "{organism}",
- "{index_size}",
- "ALFA",
+ index_stranded = os.path.join(
+ config["alfa_indexes"],
+ "{organism}",
+ "{index_size}",
+ "ALFA",
"sorted_genes.stranded.ALFA_index"),
- index_unstranded = os.path.join(config["alfa_indexes"],
- "{organism}",
- "{index_size}",
- "ALFA",
+ index_unstranded = os.path.join(
+ config["alfa_indexes"],
+ "{organism}",
+ "{index_size}",
+ "ALFA",
"sorted_genes.unstranded.ALFA_index")
params:
genome_index = "sorted_genes",
- out_dir = lambda wildcards, output: os.path.dirname(output.index_stranded)
+ out_dir = lambda wildcards, output:
+ os.path.dirname(output.index_stranded)
threads: 4
- singularity:
+ singularity:
"docker://zavolab/alfa:1.1.1-slim"
- log:
- os.path.join(config["log_dir"], "{organism}_{index_size}_generate_alfa_index.log")
+ log:
+ os.path.join(
+ config["log_dir"],
+ "{organism}_{index_size}_generate_alfa_index.log")
shell:
- """
- alfa -a {input.gtf} \
- -g {params.genome_index} \
- --chr_len {input.chr_len} \
- -p {threads} \
- -o {params.out_dir} &> {log}
- """
+ "(alfa -a {input.gtf} \
+ -g {params.genome_index} \
+ --chr_len {input.chr_len} \
+ -p {threads} \
+ -o {params.out_dir}) &> {log}"
rule alfa_qc:
- ''' Run ALFA from stranded bedgraph files '''
+ '''
+ Run ALFA from stranded bedgraph files
+ '''
input:
plus = os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
"ALFA",
"{unique}",
"{sample}_Signal.{unique}.out.plus.bg"),
minus = os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
"ALFA",
"{unique}",
"{sample}_Signal.{unique}.out.minus.bg"),
- gtf = lambda wildcards: os.path.join(config["alfa_indexes"],
- samples_table.loc[wildcards.sample, "organism"],
- str(samples_table.loc[wildcards.sample, "index_size"]),
- "ALFA",
- "sorted_genes.stranded.ALFA_index")
+ gtf = lambda wildcards:
+ os.path.join(
+ config["alfa_indexes"],
+ samples_table.loc[wildcards.sample, "organism"],
+ str(samples_table.loc[wildcards.sample, "index_size"]),
+ "ALFA",
+ "sorted_genes.stranded.ALFA_index")
output:
biotypes = os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
"ALFA",
"{unique}",
"ALFA_plots.Biotypes.pdf"),
categories = os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
"ALFA",
"{unique}",
"ALFA_plots.Categories.pdf"),
table = os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
"ALFA",
"{unique}",
"{sample}.ALFA_feature_counts.tsv")
params:
- out_dir = lambda wildcards, output: os.path.dirname(output.biotypes),
- alfa_orientation = lambda wildcards: directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]],
- in_file_plus = lambda wildcards, input: os.path.basename(input.plus),
- in_file_minus = lambda wildcards, input: os.path.basename(input.minus),
- genome_index = lambda wildcards, input: os.path.abspath(os.path.join(os.path.dirname(input.gtf), "sorted_genes")),
+ out_dir = lambda wildcards, output:
+ os.path.dirname(output.biotypes),
+ alfa_orientation = lambda wildcards:
+ directionality[samples_table.loc[
+ wildcards.sample, "kallisto_directionality"]],
+ in_file_plus = lambda wildcards, input:
+ os.path.basename(input.plus),
+ in_file_minus = lambda wildcards, input:
+ os.path.basename(input.minus),
+ genome_index = lambda wildcards, input:
+ os.path.abspath(
+ os.path.join(
+ os.path.dirname(input.gtf),
+ "sorted_genes")),
name = "{sample}"
singularity:
"docker://zavolab/alfa:1.1.1-slim"
- log:
+ log:
os.path.abspath(os.path.join(
- config["log_dir"],
- "{seqmode}",
- "{sample}",
- "alfa_qc.{unique}.log"))
+ config["log_dir"],
+ "{sample}_alfa_qc.{unique}.log"))
shell:
- """
- cd {params.out_dir}; \
- (alfa -g {params.genome_index} \
- --bedgraph {params.in_file_plus} {params.in_file_minus} {params.name} \
- -s {params.alfa_orientation}) &> {log}
- """
+ "(cd {params.out_dir}; \
+ alfa \
+ -g {params.genome_index} \
+ --bedgraph {params.in_file_plus} {params.in_file_minus} {params.name} \
+ -s {params.alfa_orientation}) &> {log}"
rule alfa_qc_all_samples:
- ''' Run ALFA from stranded bedgraph files on all samples '''
+ '''
+ Run ALFA from stranded bedgraph files on all samples
+ '''
input:
- tables = [os.path.join(
- config["output_dir"],
- samples_table.loc[sample1, "seqmode"],
- str(sample1),
- "ALFA",
- "{unique}",
- sample1 + ".ALFA_feature_counts.tsv")
- for sample1 in list(samples_table.index.values)]
-
+ tables = lambda wildcards:
+ expand(
+ os.path.join(
+ config["output_dir"],
+ "samples",
+ "{sample}",
+ "ALFA",
+ "{unique}",
+ "{sample}" + ".ALFA_feature_counts.tsv"),
+ sample=samples_table.index.values,
+ unique=wildcards.unique)
output:
biotypes = os.path.join(
config["output_dir"],
@@ -944,31 +976,31 @@ rule alfa_qc_all_samples:
"ALFA_plots.Categories.pdf")
params:
- out_dir = lambda wildcards, output: os.path.dirname(output.biotypes)
+ out_dir = lambda wildcards, output:
+ os.path.dirname(output.biotypes)
- log:
- os.path.abspath(
- os.path.join(config["log_dir"],
- "alfa_qc_all_samples.{unique}.log"))
+ log:
+ os.path.join(
+ config["log_dir"],
+ "alfa_qc_all_samples.{unique}.log")
singularity:
"docker://zavolab/alfa:1.1.1-slim"
shell:
- """
- (alfa -c {input.tables} -o {params.out_dir}) &> {log}
- """
+ "(alfa -c {input.tables} -o {params.out_dir}) &> {log}"
rule alfa_concat_results:
input:
- expand(os.path.join(
- config["output_dir"],
- "ALFA",
- "{unique_type}",
- "ALFA_plots.{annotation}.pdf"),
- unique_type = ["Unique", "UniqueMultiple"],
- annotation = ["Categories", "Biotypes"])
+ expand(
+ os.path.join(
+ config["output_dir"],
+ "ALFA",
+ "{unique}",
+ "ALFA_plots.{annotation}.pdf"),
+ unique=["Unique", "UniqueMultiple"],
+ annotation=["Categories", "Biotypes"])
output:
expand(os.path.join(
@@ -979,53 +1011,95 @@ rule alfa_concat_results:
params:
density = 300
- log:
- os.path.abspath(
- os.path.join(config["log_dir"],
- "alfa_qc_all_samples.concat.log"))
+ log:
+ os.path.join(
+ config["log_dir"],
+ "alfa_qc_all_samples.concat.log")
singularity:
"docker://zavolab/imagemagick:7.0.8"
shell:
- """
- convert -append -density {params.density} \
- {input} {output} &> {log}
- """
+ "(convert -append -density {params.density} \
+ {input} {output}) &> {log}"
+
+
+rule prepare_multiqc_config:
+ '''
+ Prepare config for the MultiQC
+ '''
+ input:
+ logo_path = os.path.abspath(
+ os.path.join(
+ "images",
+ "logo.128px.png"))
+
+ output:
+ multiqc_config = os.path.join(
+ config["output_dir"],
+ "multiqc_config.yaml")
+
+ log:
+ stderr = os.path.join(
+ config["log_dir"],
+ "prepare_multiqc_config.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "prepare_multiqc_config.stdout.log")
+
+ shell:
+ "(python scripts/rhea_multiqc_config.py \
+ --config {output.multiqc_config} \
+ --custom_logo {input.logo_path}) \
+ 1> {log.stdout} 2> {log.stderr}"
-rule prepare_files_for_report:
+rule multiqc_report:
'''
- Re-structure the results and add comments for MultiQC parsing
+ Create report with MultiQC
'''
input:
- outdir1 = expand(
+ fastqc_se = expand(
os.path.join(
config['output_dir'],
- "{seqmode}",
+ "samples",
"{sample}",
- "mate1_fastqc"),
- zip,
- sample=[i for i in list(samples_table.index.values)],
- seqmode=[samples_table.loc[i, 'seqmode']
- for i in list(samples_table.index.values)]),
+ "fastqc",
+ "{mate}"),
+ sample=samples_table.index.values,
+ mate="fq1"),
+
+ fastqc_pe = expand(
+ os.path.join(
+ config['output_dir'],
+ "samples",
+ "{sample}",
+ "fastqc",
+ "{mate}"),
+ sample=[i for i in list(
+ samples_table[samples_table['seqmode'] == 'pe'].index.values)],
+ mate="fq2"),
+
pseudoalignment = expand(
os.path.join(
config['output_dir'],
- "{seqmode}",
+ "samples",
"{sample}",
"quant_kallisto",
- "{sample}.kallisto.pseudo.sam"),
+ "{sample}.{seqmode}.kallisto.pseudo.sam"),
zip,
sample=[i for i in list(samples_table.index.values)],
seqmode=[samples_table.loc[i, 'seqmode']
for i in list(samples_table.index.values)]),
+
TIN_boxplot_PNG = os.path.join(
config['output_dir'],
"TIN_scores_boxplot.png"),
+
TIN_boxplot_PDF = os.path.join(
config['output_dir'],
"TIN_scores_boxplot.pdf"),
+
salmon_merge_genes = expand(
os.path.join(
config["output_dir"],
@@ -1033,6 +1107,7 @@ rule prepare_files_for_report:
"quantmerge",
"genes_{salmon_merge_on}.tsv"),
salmon_merge_on=["tpm", "numreads"]),
+
salmon_merge_transcripts = expand(
os.path.join(
config["output_dir"],
@@ -1040,347 +1115,137 @@ rule prepare_files_for_report:
"quantmerge",
"transcripts_{salmon_merge_on}.tsv"),
salmon_merge_on=["tpm", "numreads"]),
+
star_rpm = expand(
os.path.join(
config["output_dir"],
- "{seqmode}",
+ "samples",
"{sample}",
"STAR_coverage",
"{sample}_Signal.UniqueMultiple.str1.out.bg"),
- zip,
- sample=[i for i in list(samples_table.index.values)],
- seqmode=[samples_table.loc[i, 'seqmode']
- for i in list(samples_table.index.values)]),
+ sample=samples_table.index.values),
+
alfa_concat_out = os.path.join(
config["output_dir"],
"ALFA",
- "ALFA_plots.concat.png")
+ "ALFA_plots.concat.png"),
- output:
- samples_dir_result = directory(os.path.join(
+ multiqc_config = os.path.join(
config["output_dir"],
- "samples")),
- samples_dir_log = directory(os.path.join(
- config["log_dir"],
- "samples"))
+ "multiqc_config.yaml")
+
+ output:
+ multiqc_report = directory(
+ os.path.join(
+ config["output_dir"],
+ "multiqc_summary"))
+
params:
- results_dir = config["output_dir"],
- log_dir = config["log_dir"],
+ results_dir = os.path.join(
+ config["output_dir"]),
+ log_dir = config["log_dir"]
+
log:
stderr = os.path.join(
config["log_dir"],
- "prepare_files_for_report.stderr.log"),
+ "multiqc_report.stderr.log"),
stdout = os.path.join(
config["log_dir"],
- "prepare_files_for_report.stdout.log")
- run:
-
- # remove "single/paired end" from the results directories
- os.mkdir(output.samples_dir_result)
- # copy paired end results
- paired_end_dir = glob.glob(
- os.path.join(
- params.results_dir,
- "paired_end",
- "*"))
- for s in paired_end_dir:
- sample_name = s.split("/")[-1]
- shutil.copytree(
- s, \
- os.path.join(
- params.results_dir,
- "samples",
- sample_name))
- # copy single end results
- single_end_dir = glob.glob(
- os.path.join(
- params.results_dir,
- "single_end",
- "*"))
- for s in single_end_dir:
- sample_name = s.split("/")[-1]
- shutil.copytree(
- s, \
- os.path.join(
- params.results_dir,
- "samples",
- sample_name))
+ "multiqc_report.stdout.log")
- # remove "single/paired end" from the logs directories
- os.mkdir(output.samples_dir_log)
- # copy paired end results
- paired_end_dir = glob.glob(
- os.path.join(
- params.log_dir,
- "paired_end",
- "*"))
- for s in paired_end_dir:
- sample_name = s.split("/")[-1]
- shutil.copytree(
- s, \
- os.path.join(
- params.log_dir,
- "samples",
- sample_name))
- # copy single end results
- single_end_dir = glob.glob(
- os.path.join(
- params.log_dir,
- "single_end",
- "*"))
- for s in single_end_dir:
- sample_name = s.split("/")[-1]
- shutil.copytree(
- s, \
- os.path.join(
- params.log_dir,
- "samples",
- sample_name))
-
- # encapsulate salmon quantification results
- all_samples_dirs = glob.glob(
- os.path.join(
- params.results_dir,
- "samples",
- "*"))
- for s in all_samples_dirs:
- sample_name = s.split("/")[-1]
- shutil.move(
- os.path.join(
- s,
- "salmon_quant"),
- os.path.join(
- s,
- sample_name)
- )
- os.mkdir(os.path.join(
- s,
- "salmon_quant"))
- shutil.move(
- os.path.join(
- s,
- sample_name),
- os.path.join(
- s,
- "salmon_quant",
- sample_name)
- )
+ singularity:
+ "docker://ewels/multiqc:1.7"
- # adjust FastQC results 'Filename' field:
- fastq_zip_list = glob.glob(
- os.path.join(
- params.results_dir,
- "samples",
- "*",
- "*_fastqc",
- "*_fastqc.zip"))
- for zipfile in fastq_zip_list:
- sample_name = zipfile.split("/")[-3]
- absolute_path_zipfile = os.path.abspath(zipfile)
- zipfile_path_chunks = absolute_path_zipfile.split(os.path.sep)
- dir_path_to_zipfile = os.path.sep + os.path.join(
- (*zipfile_path_chunks[:-1]))
- with ZipFile(zipfile, 'r') as zip_f:
- zip_f.extractall(dir_path_to_zipfile)
- fastqc_data_f = os.path.join(
- zipfile[:-4],
- "fastqc_data.txt")
- with open(fastqc_data_f) as f:
- log_lines = f.read().splitlines()
- log_lines[3] = "Filename\t" + sample_name+"|"+log_lines[3].split("\t")[1]
- with open(fastqc_data_f, "w") as f:
- for i in log_lines: f.write(i+"\n")
- os.remove(zipfile)
-
- # adjust Kallisto quantification logs
- kallisto_logs = glob.glob(
- os.path.join(
- params.log_dir,
- "samples",
- "*",
- "genome_quantification_kallisto.stderr.log"))
- for kallisto_log in kallisto_logs:
- with open(kallisto_log) as f:
- log_lines = f.read().splitlines()
- temp = log_lines[8].split(".")
- log_lines[8] = temp[0] + "." + temp[2] + "." + temp[3]
- with open(kallisto_log+".MODIFIED", "w") as f:
- for i in log_lines: f.write(i+"\n")
-
- # add #-comment to all cutadapt logs:
- cutadapt_logs = glob.glob(
- os.path.join(
- params.log_dir,
- "samples",
- "*",
- "remove_*_cutadapt.stdout.log"))
- for cutadapt_log in cutadapt_logs:
- sample_name = cutadapt_log.split("/")[-2]
- with open(cutadapt_log) as f:
- log_lines = f.read().splitlines()
- log_lines[1] = log_lines[1] + " # " + sample_name
- with open(cutadapt_log, "w") as f:
- for i in log_lines: f.write(i+"\n")
-
- # adjust TIN boxplots filenames for MutliQC recognition
- os.rename(
- input.TIN_boxplot_PNG,
- os.path.join(
- params.results_dir,
- "TIN scores_mqc.png"))
- os.rename(
- input.TIN_boxplot_PDF,
- os.path.join(
- params.results_dir,
- "TIN scores_mqc.pdf"))
+ shell:
+ "(multiqc \
+ --outdir {output.multiqc_report} \
+ --config {input.multiqc_config} \
+ {params.results_dir} \
+ {params.log_dir};) \
+ 1> {log.stdout} 2> {log.stderr}"
- # adjust alfa plot filename for MutliQC recognition
- os.rename(
- input.alfa_concat_out,
- os.path.join(
- params.results_dir,
- "ALFA",
- "ALFA_plots.concat_mqc.png"))
- # remove old result directories
- shutil.rmtree(
- os.path.join(
- params.results_dir,
- "paired_end"),
- ignore_errors=False,
- onerror=None)
- shutil.rmtree(
- os.path.join(
- params.results_dir,
- "single_end"),
- ignore_errors=False,
- onerror=None)
- shutil.rmtree(
- os.path.join(
- params.log_dir,
- "paired_end"),
- ignore_errors=False,
- onerror=None)
- shutil.rmtree(
- os.path.join(
- params.log_dir,
- "single_end"),
- ignore_errors=False,
- onerror=None)
-rule prepare_MultiQC_config:
+rule sort_bed_4_big:
'''
- Prepare config for the MultiQC
+ sort bedGraphs in order to work with bedGraphtobigWig
'''
input:
- samples_dir_result = os.path.join(
+ bg = os.path.join(
config["output_dir"],
- "samples"),
- samples_dir_log = os.path.join(
- config["log_dir"],
- "samples")
+ "samples",
+ "{sample}",
+ "ALFA",
+ "{unique}",
+ "{sample}_Signal.{unique}.out.{strand}.bg")
output:
- multiqc_config = os.path.join(
- config["output_dir"],
- "MultiQC_config.yaml")
- params:
- logo_path = os.path.join(
- "..",
- "..",
- "images",
- "logo.128px.png"),
- results_dir = config["output_dir"]
+ sorted_bg = os.path.join(config["output_dir"],
+ "samples",
+ "{sample}",
+ "bigWig",
+ "{unique}",
+ "{sample}_{unique}_{strand}.sorted.bg")
+ singularity:
+ "docker://cjh4zavolab/bedtools:2.27"
log:
stderr = os.path.join(
config["log_dir"],
- "prepare_MultiQC_config.stderr.log"),
+ "samples",
+ "{sample}",
+ "sort_bg_{unique}_{strand}.stderr.log"),
stdout = os.path.join(
config["log_dir"],
- "prepare_MultiQC_config.stdout.log")
- run:
- with open(output.multiqc_config, "w") as YAML:
- YAML.write("---\n\n")
- YAML.write("title: \"Rhea\"\n")
- YAML.write("subtitle: \"RNA-Seq processing pipeline developed by the members of Zavolan Lab\"\n")
- YAML.write("intro_text: \"Short analysis title from config[analysis_title]\"\n")
- YAML.write("custom_logo: \""+params.logo_path+"\"\n")
- YAML.write("custom_logo_url: \"https://www.biozentrum.unibas.ch/research/researchgroups/overview/unit/zavolan/research-group-mihaela-zavolan/\"\n")
- YAML.write("custom_logo_title: \"ZavoLab\"\n\n")
- YAML.write("report_header_info:\n")
- YAML.write(" - Project Type: \"Snakemake workflow\"\n")
- YAML.write(" - Analysis Type: \"RNA-seq\"\n")
- YAML.write(" - Analysis Author: \"config[author_name]\"\n")
- YAML.write(" - Contact E-mail: \"config[author_email]\"\n\n")
- YAML.write("top_modules:\n\n")
- YAML.write(" - fastqc:\n")
- YAML.write(" path_filters:\n")
- YAML.write(" - \"*/mate1_fastqc/*\"\n")
- YAML.write(" - \"*/mate2_fastqc/*\"\n")
- YAML.write("\n")
- YAML.write(" - cutadapt:\n")
- YAML.write(" name: \"Cutadapt: adapter removal\"\n")
- YAML.write(" path_filters:\n")
- YAML.write(" - \"*/remove_adapters_cutadapt.stdout.log\"\n")
- YAML.write("\n")
- YAML.write(" - cutadapt:\n")
- YAML.write(" name: \"Cutadapt: polyA tails removal\"\n")
- YAML.write(" path_filters:\n")
- YAML.write(" - \"*/remove_polya_cutadapt.stdout.log\"\n")
- YAML.write("\n")
- YAML.write(" - star:\n")
- YAML.write(" path_filters:\n")
- YAML.write(" - \"*/map_genome/*\"\n")
- YAML.write("\n")
- YAML.write(" - alfa:\n")
- YAML.write(" path_filters:\n")
- YAML.write(" - \"*/ALFA_plots.concat_mqc.png\"\n")
- YAML.write("\n")
- YAML.write(" - TIN_scores:\n")
- YAML.write(" path_filters:\n")
- YAML.write(" - \"*/TIN scores_mqc.png\"\n")
- YAML.write("\n")
- YAML.write(" - salmon:\n")
- YAML.write(" path_filters:\n")
- YAML.write(" - \"*/salmon_quant/*\"\n")
- YAML.write("\n")
- YAML.write(" - kallisto:\n")
- YAML.write(" path_filters:\n")
- YAML.write(" - \"*/genome_quantification_kallisto.stderr.log.MODIFIED\"\n")
- YAML.write("\n")
- YAML.write("...")
-
-
-rule MULTIQC_report:
+ "samples",
+ "{sample}",
+ "sort_bg_{unique}_{strand}.stdout.log")
+ shell:
+ '''
+ sortBed \
+ -i {input.bg} \
+ > {output.sorted_bg}
+ '''
+
+rule prepare_bigWig:
'''
- Create report with MultiQC
+ bedGraphtobigWig, for viewing in genome browsers
'''
input:
- multiqc_config = os.path.join(
- config["output_dir"],
- "MultiQC_config.yaml")
+ sorted_bg = os.path.join(config["output_dir"],
+ "samples",
+ "{sample}",
+ "bigWig",
+ "{unique}",
+ "{sample}_{unique}_{strand}.sorted.bg"),
+ chr_sizes = lambda wildcards: os.path.join(config['star_indexes'],
+ samples_table.loc[wildcards.sample, "organism"],
+ str(samples_table.loc[wildcards.sample, "index_size"]),
+ "STAR_index",
+ "chrNameLength.txt")
output:
- MultiQC_report = directory(os.path.join(
- config["output_dir"],
- "multiqc_summary"))
- params:
- results_dir = config["output_dir"],
- log_dir = config["log_dir"]
+ bigWig = os.path.join(config["output_dir"],
+ "samples",
+ "{sample}",
+ "bigWig",
+ "{unique}",
+ "{sample}_{unique}_{strand}.bw")
+ singularity:
+ "docker://zavolab/bedgraphtobigwig:4-slim"
log:
stderr = os.path.join(
config["log_dir"],
- "MULTIQC_report.stderr.log"),
+ "samples",
+ "{sample}",
+ "bigwig_{unique}_{strand}.stderr.log"),
stdout = os.path.join(
config["log_dir"],
- "MULTIQC_report.stdout.log")
- singularity:
- "docker://ewels/multiqc:1.7"
+ "samples",
+ "{sample}",
+ "bigwig_{unique}_{strand}.stdout.log")
shell:
- """
- multiqc \
- --outdir {output.MultiQC_report} \
- --config {input.multiqc_config} \
- {params.results_dir} \
- {params.log_dir} \
- 1> {log.stdout} 2> {log.stderr}
- """
+ '''
+ bedGraphToBigWig \
+ {input.sorted_bg} \
+ {input.chr_sizes} \
+ {output.bigWig}
+ '''
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index 11a9781cbc1f74944f2d98a0ad123338074b2ae1..16ea2588c79e3b907b7d55838c9d9e54c78a723a 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -1,641 +1,1091 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<!-- Generated by graphviz version 2.38.0 (20140413.2041)
+<!-- Generated by graphviz version 2.40.1 (20161225.0304)
-->
<!-- Title: snakemake_dag Pages: 1 -->
-<svg width="2252pt" height="913pt"
- viewBox="0.00 0.00 2252.45 913.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
-<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 909)">
+<svg width="2608pt" height="846pt"
+ viewBox="0.00 0.00 2608.00 846.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 842)">
<title>snakemake_dag</title>
-<polygon fill="white" stroke="none" points="-4,4 -4,-909 2248.45,-909 2248.45,4 -4,4"/>
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-<text text-anchor="middle" x="1151" y="-15.5" font-family="sans" font-size="10.00">finish</text>
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-<text text-anchor="middle" x="1151" y="-87.5" font-family="sans" font-size="10.00">MULTIQC_report</text>
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+<title>1</title>
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+<text text-anchor="middle" x="749" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">multiqc_report</text>
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<!-- 1->0 -->
-<g id="edge1" class="edge"><title>1->0</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1154.5,-46.1043 1151,-36.1043 1147.5,-46.1044 1154.5,-46.1043"/>
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+<title>1->0</title>
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-<text text-anchor="middle" x="1151" y="-159.5" font-family="sans" font-size="10.00">prepare_MultiQC_config</text>
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+<title>2</title>
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+<text text-anchor="middle" x="1436" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
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-<g id="edge2" class="edge"><title>2->1</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1154.5,-118.104 1151,-108.104 1147.5,-118.104 1154.5,-118.104"/>
+<!-- 2->0 -->
+<g id="edge2" class="edge">
+<title>2->0</title>
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<!-- 3 -->
-<g id="node4" class="node"><title>3</title>
-<path fill="none" stroke="#c6d856" stroke-width="2" d="M1198.5,-252C1198.5,-252 1103.5,-252 1103.5,-252 1097.5,-252 1091.5,-246 1091.5,-240 1091.5,-240 1091.5,-228 1091.5,-228 1091.5,-222 1097.5,-216 1103.5,-216 1103.5,-216 1198.5,-216 1198.5,-216 1204.5,-216 1210.5,-222 1210.5,-228 1210.5,-228 1210.5,-240 1210.5,-240 1210.5,-246 1204.5,-252 1198.5,-252"/>
-<text text-anchor="middle" x="1151" y="-231.5" font-family="sans" font-size="10.00">prepare_files_for_report</text>
+<g id="node4" class="node">
+<title>3</title>
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+<text text-anchor="middle" x="1887" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
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-<!-- 3->2 -->
-<g id="edge3" class="edge"><title>3->2</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1154.5,-190.104 1151,-180.104 1147.5,-190.104 1154.5,-190.104"/>
+<!-- 3->0 -->
+<g id="edge3" class="edge">
+<title>3->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1895.521,-215.9555C1913.4085,-178.0762 1954.9614,-90.0818 1976.1206,-45.274"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1979.3263,-46.6821 1980.4315,-36.1451 1972.9965,-43.693 1979.3263,-46.6821"/>
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<!-- 4 -->
-<g id="node5" class="node"><title>4</title>
-<path fill="none" stroke="#78d856" stroke-width="2" d="M280,-324C280,-324 12,-324 12,-324 6,-324 0,-318 0,-312 0,-312 0,-300 0,-300 0,-294 6,-288 12,-288 12,-288 280,-288 280,-288 286,-288 292,-294 292,-300 292,-300 292,-312 292,-312 292,-318 286,-324 280,-324"/>
-<text text-anchor="middle" x="146" y="-309" font-family="sans" font-size="10.00">pe_fastqc</text>
-<text text-anchor="middle" x="146" y="-298" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+<g id="node5" class="node">
+<title>4</title>
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-<!-- 4->3 -->
-<g id="edge4" class="edge"><title>4->3</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1081.6,-241.725 1091.42,-237.751 1081.26,-234.733 1081.6,-241.725"/>
+<!-- 4->0 -->
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+<title>4->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1544.3856,-215.7719C1552.4206,-195.4198 1568.1264,-162.8694 1592,-144 1703.0743,-56.2085 1876.4655,-29.0029 1951.8817,-21.0621"/>
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<!-- 5 -->
-<g id="node6" class="node"><title>5</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M602,-324C602,-324 322,-324 322,-324 316,-324 310,-318 310,-312 310,-312 310,-300 310,-300 310,-294 316,-288 322,-288 322,-288 602,-288 602,-288 608,-288 614,-294 614,-300 614,-300 614,-312 614,-312 614,-318 608,-324 602,-324"/>
-<text text-anchor="middle" x="462" y="-309" font-family="sans" font-size="10.00">fastqc</text>
-<text text-anchor="middle" x="462" y="-298" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+<g id="node6" class="node">
+<title>5</title>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M2019,-252C2019,-252 1959,-252 1959,-252 1953,-252 1947,-246 1947,-240 1947,-240 1947,-228 1947,-228 1947,-222 1953,-216 1959,-216 1959,-216 2019,-216 2019,-216 2025,-216 2031,-222 2031,-228 2031,-228 2031,-240 2031,-240 2031,-246 2025,-252 2019,-252"/>
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-<!-- 5->3 -->
-<g id="edge5" class="edge"><title>5->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M614.42,-289.384C618.998,-288.917 623.533,-288.455 628,-288 790.391,-271.457 981.161,-252.159 1081.39,-242.031"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1081.79,-245.508 1091.39,-241.02 1081.09,-238.543 1081.79,-245.508"/>
+<!-- 5->0 -->
+<g id="edge5" class="edge">
+<title>5->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1989,-215.9555C1989,-178.3938 1989,-91.5541 1989,-46.4103"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1992.5001,-46.145 1989,-36.1451 1985.5001,-46.1451 1992.5001,-46.145"/>
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<!-- 6 -->
-<g id="node7" class="node"><title>6</title>
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-<text text-anchor="middle" x="1322" y="-447.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
+<g id="node7" class="node">
+<title>6</title>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M2121,-252C2121,-252 2061,-252 2061,-252 2055,-252 2049,-246 2049,-240 2049,-240 2049,-228 2049,-228 2049,-222 2055,-216 2061,-216 2061,-216 2121,-216 2121,-216 2127,-216 2133,-222 2133,-228 2133,-228 2133,-240 2133,-240 2133,-246 2127,-252 2121,-252"/>
+<text text-anchor="middle" x="2091" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
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-<!-- 6->3 -->
-<g id="edge6" class="edge"><title>6->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1328.46,-431.931C1339.29,-400.128 1356.95,-331.131 1325,-288 1301.2,-255.876 1258.39,-242.563 1221.19,-237.312"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1221.22,-233.789 1210.87,-236.035 1220.36,-240.736 1221.22,-233.789"/>
+<!-- 6->0 -->
+<g id="edge6" class="edge">
+<title>6->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2082.479,-215.9555C2064.5915,-178.0762 2023.0386,-90.0818 2001.8794,-45.274"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2005.0035,-43.693 1997.5685,-36.1451 1998.6737,-46.6821 2005.0035,-43.693"/>
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<!-- 7 -->
-<g id="node8" class="node"><title>7</title>
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-<text text-anchor="middle" x="620" y="-447.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
+<g id="node8" class="node">
+<title>7</title>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M2344,-252C2344,-252 2284,-252 2284,-252 2278,-252 2272,-246 2272,-240 2272,-240 2272,-228 2272,-228 2272,-222 2278,-216 2284,-216 2284,-216 2344,-216 2344,-216 2350,-216 2356,-222 2356,-228 2356,-228 2356,-240 2356,-240 2356,-246 2350,-252 2344,-252"/>
+<text text-anchor="middle" x="2314" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
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-<g id="edge7" class="edge"><title>7->3</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1081.59,-241.672 1091.4,-237.678 1081.24,-234.681 1081.59,-241.672"/>
+<!-- 7->0 -->
+<g id="edge7" class="edge">
+<title>7->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2287.064,-215.9709C2242.2713,-186.0057 2149.6162,-124.0906 2071,-72 2055.9379,-62.0199 2039.2903,-51.0464 2024.9527,-41.6132"/>
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<!-- 8 -->
-<g id="node9" class="node"><title>8</title>
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-<text text-anchor="middle" x="1417" y="-375.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
+<g id="node9" class="node">
+<title>8</title>
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-<!-- 8->3 -->
-<g id="edge8" class="edge"><title>8->3</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1221.03,-236.678 1210.66,-238.84 1220.11,-243.618 1221.03,-236.678"/>
+<!-- 8->0 -->
+<g id="edge8" class="edge">
+<title>8->0</title>
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+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2015.5478,-41.012 2006.137,-36.1451 2010.4587,-45.8184 2015.5478,-41.012"/>
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<!-- 9 -->
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-<text text-anchor="middle" x="738" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
+<g id="node10" class="node">
+<title>9</title>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M2484,-252C2484,-252 2424,-252 2424,-252 2418,-252 2412,-246 2412,-240 2412,-240 2412,-228 2412,-228 2412,-222 2418,-216 2424,-216 2424,-216 2484,-216 2484,-216 2490,-216 2496,-222 2496,-228 2496,-228 2496,-240 2496,-240 2496,-246 2490,-252 2484,-252"/>
+<text text-anchor="middle" x="2454" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
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+<!-- 9->0 -->
+<g id="edge9" class="edge">
+<title>9->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2416.582,-215.9588C2353.6882,-185.7174 2222.6935,-123.0863 2111,-72 2082.3629,-58.902 2049.7344,-44.4861 2025.4304,-33.8461"/>
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<!-- 10 -->
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-<text text-anchor="middle" x="897" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
-<text text-anchor="middle" x="897" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
+<g id="node11" class="node">
+<title>10</title>
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+<text text-anchor="middle" x="39" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
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-<!-- 10->3 -->
-<g id="edge10" class="edge"><title>10->3</title>
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+<!-- 10->1 -->
+<g id="edge10" class="edge">
+<title>10->1</title>
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<!-- 11 -->
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-<text text-anchor="middle" x="1065" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
-<text text-anchor="middle" x="1065" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
+<g id="node12" class="node">
+<title>11</title>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M342,-686.5C342,-686.5 312,-686.5 312,-686.5 306,-686.5 300,-680.5 300,-674.5 300,-674.5 300,-662.5 300,-662.5 300,-656.5 306,-650.5 312,-650.5 312,-650.5 342,-650.5 342,-650.5 348,-650.5 354,-656.5 354,-662.5 354,-662.5 354,-674.5 354,-674.5 354,-680.5 348,-686.5 342,-686.5"/>
+<text text-anchor="middle" x="327" y="-666" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
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-<!-- 11->3 -->
-<g id="edge11" class="edge"><title>11->3</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1124.44,-261.132 1129.99,-252.104 1120.02,-255.703 1124.44,-261.132"/>
+<!-- 11->1 -->
+<g id="edge11" class="edge">
+<title>11->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M299.8159,-664.4991C238.3531,-653.7581 94,-618.2825 94,-522 94,-522 94,-522 94,-234 94,-193.1184 82.3655,-171.0709 113,-144 156.6446,-105.4325 557.5495,-93.7918 699.4823,-90.8625"/>
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<!-- 12 -->
-<g id="node13" class="node"><title>12</title>
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-<text text-anchor="middle" x="1238" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
-<text text-anchor="middle" x="1238" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
+<g id="node13" class="node">
+<title>12</title>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1086,-761C1086,-761 1056,-761 1056,-761 1050,-761 1044,-755 1044,-749 1044,-749 1044,-737 1044,-737 1044,-731 1050,-725 1056,-725 1056,-725 1086,-725 1086,-725 1092,-725 1098,-731 1098,-737 1098,-737 1098,-749 1098,-749 1098,-755 1092,-761 1086,-761"/>
+<text text-anchor="middle" x="1071" y="-740.5" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
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-<!-- 12->3 -->
-<g id="edge12" class="edge"><title>12->3</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1182.24,-255.646 1172.26,-252.104 1177.86,-261.1 1182.24,-255.646"/>
+<!-- 12->1 -->
+<g id="edge12" class="edge">
+<title>12->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1098.2825,-732.7686C1144.6847,-713.3904 1234,-666.6546 1234,-594 1234,-594 1234,-594 1234,-522 1234,-481.1184 1226.1917,-471.3199 1215,-432 1210.343,-415.6386 1207.049,-412.2447 1202,-396 1167.6366,-285.4396 1222.5332,-220.9184 1136,-144 1111.1171,-121.8819 896.8409,-101.9327 798.2592,-93.8315"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="798.4921,-90.339 788.2412,-93.0164 797.9243,-97.316 798.4921,-90.339"/>
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<!-- 13 -->
-<g id="node14" class="node"><title>13</title>
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-<text text-anchor="middle" x="1958" y="-591.5" font-family="sans" font-size="10.00">star_rpm</text>
+<g id="node14" class="node">
+<title>13</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M331,-252C331,-252 189,-252 189,-252 183,-252 177,-246 177,-240 177,-240 177,-228 177,-228 177,-222 183,-216 189,-216 189,-216 331,-216 331,-216 337,-216 343,-222 343,-228 343,-228 343,-240 343,-240 343,-246 337,-252 331,-252"/>
+<text text-anchor="middle" x="260" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
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-<!-- 13->3 -->
-<g id="edge13" class="edge"><title>13->3</title>
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-<g id="node43" class="node"><title>42</title>
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-<text text-anchor="middle" x="2149" y="-525" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
-<text text-anchor="middle" x="2149" y="-514" font-family="sans" font-size="10.00">unique: Unique</text>
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-<!-- 13->42 -->
-<g id="edge71" class="edge"><title>13->42</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1985.77,-582.821C2013.67,-572.597 2057.46,-556.549 2092.66,-543.648"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="2094.16,-546.828 2102.34,-540.1 2091.75,-540.255 2094.16,-546.828"/>
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-<!-- 45 -->
-<g id="node46" class="node"><title>45</title>
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-<text text-anchor="middle" x="1879" y="-525" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
-<text text-anchor="middle" x="1879" y="-514" font-family="sans" font-size="10.00">unique: UniqueMultiple</text>
-</g>
-<!-- 13->45 -->
-<g id="edge74" class="edge"><title>13->45</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1938.47,-575.697C1928.62,-566.965 1916.51,-556.24 1905.8,-546.75"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1908.11,-544.117 1898.3,-540.104 1903.47,-549.356 1908.11,-544.117"/>
+<!-- 13->1 -->
+<g id="edge13" class="edge">
+<title>13->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M265.5283,-215.7016C272.9236,-194.6395 288.1899,-160.7974 314,-144 376.6805,-103.2072 599.5224,-93.222 699.6508,-90.7842"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="699.89,-94.2798 709.8076,-90.5527 699.7305,-87.2816 699.89,-94.2798"/>
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<!-- 14 -->
-<g id="node15" class="node"><title>14</title>
-<path fill="none" stroke="#56d8d8" stroke-width="2" d="M1652.5,-612C1652.5,-612 1621.5,-612 1621.5,-612 1615.5,-612 1609.5,-606 1609.5,-600 1609.5,-600 1609.5,-588 1609.5,-588 1609.5,-582 1615.5,-576 1621.5,-576 1621.5,-576 1652.5,-576 1652.5,-576 1658.5,-576 1664.5,-582 1664.5,-588 1664.5,-588 1664.5,-600 1664.5,-600 1664.5,-606 1658.5,-612 1652.5,-612"/>
-<text text-anchor="middle" x="1637" y="-591.5" font-family="sans" font-size="10.00">star_rpm</text>
-</g>
-<!-- 14->3 -->
-<g id="edge14" class="edge"><title>14->3</title>
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-<!-- 44 -->
-<g id="node45" class="node"><title>44</title>
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-<text text-anchor="middle" x="1731" y="-525" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
-<text text-anchor="middle" x="1731" y="-514" font-family="sans" font-size="10.00">unique: Unique</text>
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-<!-- 14->44 -->
-<g id="edge73" class="edge"><title>14->44</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1660.24,-575.697C1672.19,-566.796 1686.92,-555.823 1699.85,-546.199"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1702.1,-548.884 1708.03,-540.104 1697.92,-543.27 1702.1,-548.884"/>
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-<!-- 46 -->
-<g id="node47" class="node"><title>46</title>
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-<text text-anchor="middle" x="1583" y="-525" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
-<text text-anchor="middle" x="1583" y="-514" font-family="sans" font-size="10.00">unique: UniqueMultiple</text>
+<g id="node15" class="node">
+<title>14</title>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M499,-252C499,-252 373,-252 373,-252 367,-252 361,-246 361,-240 361,-240 361,-228 361,-228 361,-222 367,-216 373,-216 373,-216 499,-216 499,-216 505,-216 511,-222 511,-228 511,-228 511,-240 511,-240 511,-246 505,-252 499,-252"/>
+<text text-anchor="middle" x="436" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
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-<!-- 14->46 -->
-<g id="edge75" class="edge"><title>14->46</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1605.07,-545.884 1596.19,-540.104 1599.53,-550.16 1605.07,-545.884"/>
+<!-- 14->1 -->
+<g id="edge14" class="edge">
+<title>14->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M369.4141,-215.9556C351.9848,-207.8798 335.2289,-196.3513 325,-180 316.5145,-166.4355 314.4251,-156.0071 325,-144 349.4441,-116.2452 592.9552,-98.97 699.5097,-92.6844"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="699.9056,-96.1674 709.6857,-92.0931 699.4995,-89.1792 699.9056,-96.1674"/>
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<!-- 15 -->
-<g id="node16" class="node"><title>15</title>
-<path fill="none" stroke="#d6d856" stroke-width="2" d="M1780.5,-324C1780.5,-324 1703.5,-324 1703.5,-324 1697.5,-324 1691.5,-318 1691.5,-312 1691.5,-312 1691.5,-300 1691.5,-300 1691.5,-294 1697.5,-288 1703.5,-288 1703.5,-288 1780.5,-288 1780.5,-288 1786.5,-288 1792.5,-294 1792.5,-300 1792.5,-300 1792.5,-312 1792.5,-312 1792.5,-318 1786.5,-324 1780.5,-324"/>
-<text text-anchor="middle" x="1742" y="-303.5" font-family="sans" font-size="10.00">alfa_concat_results</text>
+<g id="node16" class="node">
+<title>15</title>
+<path fill="none" stroke="#56d863" stroke-width="2" d="M1114.5,-180C1114.5,-180 1049.5,-180 1049.5,-180 1043.5,-180 1037.5,-174 1037.5,-168 1037.5,-168 1037.5,-156 1037.5,-156 1037.5,-150 1043.5,-144 1049.5,-144 1049.5,-144 1114.5,-144 1114.5,-144 1120.5,-144 1126.5,-150 1126.5,-156 1126.5,-156 1126.5,-168 1126.5,-168 1126.5,-174 1120.5,-180 1114.5,-180"/>
+<text text-anchor="middle" x="1082" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">plot_TIN_scores</text>
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-<!-- 15->3 -->
-<g id="edge15" class="edge"><title>15->3</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1221.09,-239.777 1210.74,-242.076 1220.26,-246.728 1221.09,-239.777"/>
+<!-- 15->1 -->
+<g id="edge15" class="edge">
+<title>15->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1037.3555,-147.8586C1032.5291,-146.4858 1027.6748,-145.1705 1023,-144 945.2348,-124.5279 853.6226,-107.6826 798.4903,-98.1938"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="798.7454,-94.6867 788.2987,-96.452 797.5662,-101.5866 798.7454,-94.6867"/>
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<!-- 16 -->
-<g id="node17" class="node"><title>16</title>
-<path fill="none" stroke="#97d856" stroke-width="2" d="M1322,-830.5C1322,-830.5 1210,-830.5 1210,-830.5 1204,-830.5 1198,-824.5 1198,-818.5 1198,-818.5 1198,-806.5 1198,-806.5 1198,-800.5 1204,-794.5 1210,-794.5 1210,-794.5 1322,-794.5 1322,-794.5 1328,-794.5 1334,-800.5 1334,-806.5 1334,-806.5 1334,-818.5 1334,-818.5 1334,-824.5 1328,-830.5 1322,-830.5"/>
-<text text-anchor="middle" x="1266" y="-810" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
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-<!-- 16->6 -->
-<g id="edge16" class="edge"><title>16->6</title>
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-<g id="node21" class="node"><title>20</title>
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-<text text-anchor="middle" x="1057" y="-375.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
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-<!-- 16->20 -->
-<g id="edge40" class="edge"><title>16->20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1258.31,-794.093C1247.21,-767.328 1228,-714.21 1228,-667 1228,-667 1228,-667 1228,-593 1228,-552.553 1230.02,-538.557 1209,-504 1181.67,-459.06 1132.24,-422.965 1097.17,-401.329"/>
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-<!-- 22 -->
-<g id="node23" class="node"><title>22</title>
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-<text text-anchor="middle" x="1778" y="-735.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
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-<!-- 16->22 -->
-<g id="edge45" class="edge"><title>16->22</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1711.83,-751.905 1721.24,-747.037 1710.85,-744.974 1711.83,-751.905"/>
+<g id="node17" class="node">
+<title>16</title>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M805,-180C805,-180 693,-180 693,-180 687,-180 681,-174 681,-168 681,-168 681,-156 681,-156 681,-150 687,-144 693,-144 693,-144 805,-144 805,-144 811,-144 817,-150 817,-156 817,-156 817,-168 817,-168 817,-174 811,-180 805,-180"/>
+<text text-anchor="middle" x="749" y="-165" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="749" y="-154" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: tpm</text>
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+<!-- 16->1 -->
+<g id="edge16" class="edge">
+<title>16->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M749,-143.8314C749,-136.131 749,-126.9743 749,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="752.5001,-118.4132 749,-108.4133 745.5001,-118.4133 752.5001,-118.4132"/>
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<!-- 17 -->
-<g id="node18" class="node"><title>17</title>
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-<text text-anchor="middle" x="1146" y="-519.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
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+<g id="node18" class="node">
+<title>17</title>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M968.5,-180C968.5,-180 847.5,-180 847.5,-180 841.5,-180 835.5,-174 835.5,-168 835.5,-168 835.5,-156 835.5,-156 835.5,-150 841.5,-144 847.5,-144 847.5,-144 968.5,-144 968.5,-144 974.5,-144 980.5,-150 980.5,-156 980.5,-156 980.5,-168 980.5,-168 980.5,-174 974.5,-180 968.5,-180"/>
+<text text-anchor="middle" x="908" y="-165" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="908" y="-154" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: numreads</text>
+</g>
+<!-- 17->1 -->
+<g id="edge17" class="edge">
+<title>17->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M867.8776,-143.8314C846.4653,-134.1352 819.9543,-122.1303 797.4052,-111.9193"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="798.5636,-108.6018 788.0103,-107.665 795.676,-114.9785 798.5636,-108.6018"/>
</g>
<!-- 18 -->
-<g id="node19" class="node"><title>18</title>
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-<text text-anchor="middle" x="707" y="-810" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
-</g>
-<!-- 18->7 -->
-<g id="edge18" class="edge"><title>18->7</title>
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+<g id="node19" class="node">
+<title>18</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M477.5,-180C477.5,-180 346.5,-180 346.5,-180 340.5,-180 334.5,-174 334.5,-168 334.5,-168 334.5,-156 334.5,-156 334.5,-150 340.5,-144 346.5,-144 346.5,-144 477.5,-144 477.5,-144 483.5,-144 489.5,-150 489.5,-156 489.5,-156 489.5,-168 489.5,-168 489.5,-174 483.5,-180 477.5,-180"/>
+<text text-anchor="middle" x="412" y="-165" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="412" y="-154" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: tpm</text>
+</g>
+<!-- 18->1 -->
+<g id="edge18" class="edge">
+<title>18->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M489.7378,-145.3913C554.5175,-131.5512 644.8076,-112.2607 699.9542,-100.4786"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="700.7802,-103.8812 709.8282,-98.369 699.3176,-97.0357 700.7802,-103.8812"/>
</g>
-<!-- 21 -->
-<g id="node22" class="node"><title>21</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M948.5,-396C948.5,-396 861.5,-396 861.5,-396 855.5,-396 849.5,-390 849.5,-384 849.5,-384 849.5,-372 849.5,-372 849.5,-366 855.5,-360 861.5,-360 861.5,-360 948.5,-360 948.5,-360 954.5,-360 960.5,-366 960.5,-372 960.5,-372 960.5,-384 960.5,-384 960.5,-390 954.5,-396 948.5,-396"/>
-<text text-anchor="middle" x="905" y="-375.5" font-family="sans" font-size="10.00">quantification_salmon</text>
+<!-- 19 -->
+<g id="node20" class="node">
+<title>19</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M650.5,-180C650.5,-180 519.5,-180 519.5,-180 513.5,-180 507.5,-174 507.5,-168 507.5,-168 507.5,-156 507.5,-156 507.5,-150 513.5,-144 519.5,-144 519.5,-144 650.5,-144 650.5,-144 656.5,-144 662.5,-150 662.5,-156 662.5,-156 662.5,-168 662.5,-168 662.5,-174 656.5,-180 650.5,-180"/>
+<text text-anchor="middle" x="585" y="-165" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="585" y="-154" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: numreads</text>
+</g>
+<!-- 19->1 -->
+<g id="edge19" class="edge">
+<title>19->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M626.3841,-143.8314C648.902,-133.9455 676.8866,-121.6595 700.4333,-111.322"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="702.1378,-114.3962 709.8872,-107.1715 699.3238,-107.9867 702.1378,-114.3962"/>
</g>
-<!-- 18->21 -->
-<g id="edge42" class="edge"><title>18->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M707,-794.151C707,-767.022 707,-712.909 707,-667 707,-667 707,-667 707,-593 707,-552.553 703.64,-537.704 726,-504 757.754,-456.137 814.637,-421.138 855.772,-400.545"/>
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+<!-- 20 -->
+<g id="node21" class="node">
+<title>20</title>
+<path fill="none" stroke="#d8c356" stroke-width="2" d="M933.5,-468C933.5,-468 902.5,-468 902.5,-468 896.5,-468 890.5,-462 890.5,-456 890.5,-456 890.5,-444 890.5,-444 890.5,-438 896.5,-432 902.5,-432 902.5,-432 933.5,-432 933.5,-432 939.5,-432 945.5,-438 945.5,-444 945.5,-444 945.5,-456 945.5,-456 945.5,-462 939.5,-468 933.5,-468"/>
+<text text-anchor="middle" x="918" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
+</g>
+<!-- 20->1 -->
+<g id="edge20" class="edge">
+<title>20->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M931.5988,-431.8479C968.189,-380.6481 1061.2944,-233.0369 990,-144 966.4535,-114.5937 861.6864,-100.1145 798.2917,-93.9252"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="798.3938,-90.4194 788.1099,-92.9674 797.7381,-97.3887 798.3938,-90.4194"/>
+</g>
+<!-- 48 -->
+<g id="node49" class="node">
+<title>48</title>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M1357,-396C1357,-396 1251,-396 1251,-396 1245,-396 1239,-390 1239,-384 1239,-384 1239,-372 1239,-372 1239,-366 1245,-360 1251,-360 1251,-360 1357,-360 1357,-360 1363,-360 1369,-366 1369,-372 1369,-372 1369,-384 1369,-384 1369,-390 1363,-396 1357,-396"/>
+<text text-anchor="middle" x="1304" y="-381" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="1304" y="-370" font-family="sans" font-size="10.00" fill="#000000">unique: Unique</text>
+</g>
+<!-- 20->48 -->
+<g id="edge89" class="edge">
+<title>20->48</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M945.5144,-435.5149C948.6601,-434.1905 951.8639,-432.9809 955,-432 1004.6733,-416.4629 1141.9601,-397.7834 1228.8032,-386.9632"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1229.379,-390.4187 1238.8727,-385.7156 1228.5182,-383.4718 1229.379,-390.4187"/>
+</g>
+<!-- 49 -->
+<g id="node50" class="node">
+<title>49</title>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M1518,-396C1518,-396 1412,-396 1412,-396 1406,-396 1400,-390 1400,-384 1400,-384 1400,-372 1400,-372 1400,-366 1406,-360 1412,-360 1412,-360 1518,-360 1518,-360 1524,-360 1530,-366 1530,-372 1530,-372 1530,-384 1530,-384 1530,-390 1524,-396 1518,-396"/>
+<text text-anchor="middle" x="1465" y="-381" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="1465" y="-370" font-family="sans" font-size="10.00" fill="#000000">unique: UniqueMultiple</text>
+</g>
+<!-- 20->49 -->
+<g id="edge90" class="edge">
+<title>20->49</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M945.8624,-435.13C948.8882,-433.9145 951.9698,-432.8349 955,-432 1136.9022,-381.8842 1191.2857,-423.1619 1378,-396 1381.8397,-395.4414 1385.7649,-394.8188 1389.7216,-394.1502"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1390.3544,-397.5926 1399.5915,-392.4034 1389.1345,-390.6997 1390.3544,-397.5926"/>
</g>
-<!-- 24 -->
-<g id="node25" class="node"><title>24</title>
-<path fill="none" stroke="#d8bc56" stroke-width="2" d="M1619.5,-756C1619.5,-756 1546.5,-756 1546.5,-756 1540.5,-756 1534.5,-750 1534.5,-744 1534.5,-744 1534.5,-732 1534.5,-732 1534.5,-726 1540.5,-720 1546.5,-720 1546.5,-720 1619.5,-720 1619.5,-720 1625.5,-720 1631.5,-726 1631.5,-732 1631.5,-732 1631.5,-744 1631.5,-744 1631.5,-750 1625.5,-756 1619.5,-756"/>
-<text text-anchor="middle" x="1583" y="-735.5" font-family="sans" font-size="10.00">map_genome_star</text>
+<!-- 21 -->
+<g id="node22" class="node">
+<title>21</title>
+<path fill="none" stroke="#d8c356" stroke-width="2" d="M1479.5,-468C1479.5,-468 1448.5,-468 1448.5,-468 1442.5,-468 1436.5,-462 1436.5,-456 1436.5,-456 1436.5,-444 1436.5,-444 1436.5,-438 1442.5,-432 1448.5,-432 1448.5,-432 1479.5,-432 1479.5,-432 1485.5,-432 1491.5,-438 1491.5,-444 1491.5,-444 1491.5,-456 1491.5,-456 1491.5,-462 1485.5,-468 1479.5,-468"/>
+<text text-anchor="middle" x="1464" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
+</g>
+<!-- 21->1 -->
+<g id="edge21" class="edge">
+<title>21->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1436.2499,-447.2272C1380.7817,-441.1241 1259.0457,-424.7366 1230,-396 1148.0822,-314.9538 1254.8249,-220.8967 1169,-144 1141.7766,-119.6086 903.3729,-100.5248 798.336,-93.2227"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="798.5158,-89.7269 788.2992,-92.5327 798.0356,-96.7104 798.5158,-89.7269"/>
+</g>
+<!-- 50 -->
+<g id="node51" class="node">
+<title>50</title>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M1916,-396C1916,-396 1810,-396 1810,-396 1804,-396 1798,-390 1798,-384 1798,-384 1798,-372 1798,-372 1798,-366 1804,-360 1810,-360 1810,-360 1916,-360 1916,-360 1922,-360 1928,-366 1928,-372 1928,-372 1928,-384 1928,-384 1928,-390 1922,-396 1916,-396"/>
+<text text-anchor="middle" x="1863" y="-381" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="1863" y="-370" font-family="sans" font-size="10.00" fill="#000000">unique: Unique</text>
+</g>
+<!-- 21->50 -->
+<g id="edge91" class="edge">
+<title>21->50</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1491.7401,-444.9943C1552.2965,-434.0668 1698.0829,-407.7595 1787.8967,-391.5525"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1788.5344,-394.994 1797.7539,-389.7737 1787.2912,-388.1053 1788.5344,-394.994"/>
+</g>
+<!-- 51 -->
+<g id="node52" class="node">
+<title>51</title>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M2064,-396C2064,-396 1958,-396 1958,-396 1952,-396 1946,-390 1946,-384 1946,-384 1946,-372 1946,-372 1946,-366 1952,-360 1958,-360 1958,-360 2064,-360 2064,-360 2070,-360 2076,-366 2076,-372 2076,-372 2076,-384 2076,-384 2076,-390 2070,-396 2064,-396"/>
+<text text-anchor="middle" x="2011" y="-381" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="2011" y="-370" font-family="sans" font-size="10.00" fill="#000000">unique: UniqueMultiple</text>
+</g>
+<!-- 21->51 -->
+<g id="edge92" class="edge">
+<title>21->51</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1491.6324,-448.0589C1563.3904,-442.7615 1761.6282,-426.4906 1935.8683,-396.086"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1936.4844,-399.5315 1945.7238,-394.3464 1935.2676,-392.638 1936.4844,-399.5315"/>
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-<!-- 18->24 -->
-<g id="edge48" class="edge"><title>18->24</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M767.211,-806.517C927.87,-793.22 1365.27,-757.02 1524.24,-743.863"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1524.63,-747.343 1534.31,-743.03 1524.05,-740.367 1524.63,-747.343"/>
+<!-- 22 -->
+<g id="node23" class="node">
+<title>22</title>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M1689.5,-180C1689.5,-180 1612.5,-180 1612.5,-180 1606.5,-180 1600.5,-174 1600.5,-168 1600.5,-168 1600.5,-156 1600.5,-156 1600.5,-150 1606.5,-144 1612.5,-144 1612.5,-144 1689.5,-144 1689.5,-144 1695.5,-144 1701.5,-150 1701.5,-156 1701.5,-156 1701.5,-168 1701.5,-168 1701.5,-174 1695.5,-180 1689.5,-180"/>
+<text text-anchor="middle" x="1651" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">alfa_concat_results</text>
</g>
-<!-- 19 -->
-<g id="node20" class="node"><title>19</title>
-<path fill="none" stroke="#5673d8" stroke-width="2" d="M1450,-540C1450,-540 1374,-540 1374,-540 1368,-540 1362,-534 1362,-528 1362,-528 1362,-516 1362,-516 1362,-510 1368,-504 1374,-504 1374,-504 1450,-504 1450,-504 1456,-504 1462,-510 1462,-516 1462,-516 1462,-528 1462,-528 1462,-534 1456,-540 1450,-540"/>
-<text text-anchor="middle" x="1412" y="-519.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
-</g>
-<!-- 19->8 -->
-<g id="edge20" class="edge"><title>19->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1412.67,-503.815C1413.06,-493.443 1413.57,-479.963 1414,-468 1414.74,-447.272 1415.53,-423.828 1416.11,-406.206"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1419.61,-406.172 1416.45,-396.063 1412.62,-405.942 1419.61,-406.172"/>
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-<!-- 20->9 -->
-<g id="edge21" class="edge"><title>20->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M993.212,-363.003C942.204,-351.81 870.473,-336.069 816.041,-324.125"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="816.606,-320.666 806.088,-321.941 815.105,-327.503 816.606,-320.666"/>
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-<!-- 20->10 -->
-<g id="edge23" class="edge"><title>20->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1017.86,-359.876C995.987,-350.307 968.543,-338.3 945.338,-328.148"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="946.578,-324.87 936.013,-324.068 943.772,-331.283 946.578,-324.87"/>
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-<!-- 20->11 -->
-<g id="edge25" class="edge"><title>20->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1058.98,-359.697C1059.86,-351.983 1060.92,-342.712 1061.9,-334.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1065.39,-334.437 1063.05,-324.104 1058.43,-333.642 1065.39,-334.437"/>
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-<!-- 20->12 -->
-<g id="edge27" class="edge"><title>20->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1101.28,-359.876C1126.35,-350.179 1157.9,-337.98 1184.37,-327.743"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1185.8,-330.94 1193.87,-324.068 1183.28,-324.411 1185.8,-330.94"/>
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-<!-- 21->9 -->
-<g id="edge22" class="edge"><title>21->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M864.147,-359.876C841.216,-350.264 812.418,-338.193 788.13,-328.013"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="789.296,-324.706 778.72,-324.068 786.59,-331.162 789.296,-324.706"/>
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-<!-- 21->10 -->
-<g id="edge24" class="edge"><title>21->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M903.022,-359.697C902.141,-351.983 901.081,-342.712 900.099,-334.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="903.568,-333.642 898.955,-324.104 896.613,-334.437 903.568,-333.642"/>
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-<!-- 21->11 -->
-<g id="edge26" class="edge"><title>21->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M944.14,-359.876C966.013,-350.307 993.457,-338.3 1016.66,-328.148"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1018.23,-331.283 1025.99,-324.068 1015.42,-324.87 1018.23,-331.283"/>
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-<!-- 21->12 -->
-<g id="edge28" class="edge"><title>21->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M960.512,-365.182C968.722,-363.44 977.081,-361.671 985,-360 1040.05,-348.385 1101.85,-335.436 1150.6,-325.245"/>
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-<!-- 22->13 -->
-<g id="edge29" class="edge"><title>22->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1834.89,-734.427C1872.5,-729.541 1919.73,-716.711 1947,-684 1961.13,-667.049 1962.99,-641.583 1961.83,-622.229"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1965.31,-621.847 1960.93,-612.198 1958.33,-622.469 1965.31,-621.847"/>
+<!-- 22->1 -->
+<g id="edge22" class="edge">
+<title>22->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1600.2464,-157.9487C1441.5815,-145.2837 956.1521,-106.5354 798.8019,-93.9753"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="798.7299,-90.4585 788.4831,-93.1516 798.1729,-97.4363 798.7299,-90.4585"/>
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<!-- 23 -->
-<g id="node24" class="node"><title>23</title>
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-<text text-anchor="middle" x="1851" y="-669" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
-<text text-anchor="middle" x="1851" y="-658" font-family="sans" font-size="10.00">seqmode: paired_end</text>
+<g id="node24" class="node">
+<title>23</title>
+<path fill="none" stroke="#5673d8" stroke-width="2" d="M227.5,-180C227.5,-180 134.5,-180 134.5,-180 128.5,-180 122.5,-174 122.5,-168 122.5,-168 122.5,-156 122.5,-156 122.5,-150 128.5,-144 134.5,-144 134.5,-144 227.5,-144 227.5,-144 233.5,-144 239.5,-150 239.5,-156 239.5,-156 239.5,-168 239.5,-168 239.5,-174 233.5,-180 227.5,-180"/>
+<text text-anchor="middle" x="181" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">prepare_multiqc_config</text>
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-<!-- 22->23 -->
-<g id="edge46" class="edge"><title>22->23</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1796.04,-719.697C1805.06,-711.05 1816.12,-700.449 1825.94,-691.027"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1828.37,-693.552 1833.16,-684.104 1823.52,-688.499 1828.37,-693.552"/>
+<!-- 23->1 -->
+<g id="edge23" class="edge">
+<title>23->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M239.8233,-146.7826C244.6034,-145.7638 249.3728,-144.8191 254,-144 415.9214,-115.3363 610.5087,-99.4553 699.8193,-93.1863"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="700.1898,-96.6692 709.9241,-92.4867 699.7062,-89.6859 700.1898,-96.6692"/>
</g>
-<!-- 31 -->
-<g id="node32" class="node"><title>31</title>
-<path fill="none" stroke="#56d86b" stroke-width="2" d="M1579,-612C1579,-612 1491,-612 1491,-612 1485,-612 1479,-606 1479,-600 1479,-600 1479,-588 1479,-588 1479,-582 1485,-576 1491,-576 1491,-576 1579,-576 1579,-576 1585,-576 1591,-582 1591,-588 1591,-588 1591,-600 1591,-600 1591,-606 1585,-612 1579,-612"/>
-<text text-anchor="middle" x="1535" y="-591.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
-</g>
-<!-- 22->31 -->
-<g id="edge54" class="edge"><title>22->31</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1762.74,-719.786C1744.5,-700.11 1712.25,-668.045 1679,-648 1654.93,-633.488 1626.23,-621.935 1600.82,-613.367"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1601.85,-610.021 1591.25,-610.229 1599.67,-616.672 1601.85,-610.021"/>
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-<!-- 23->13 -->
-<g id="edge30" class="edge"><title>23->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1877.18,-647.876C1891.04,-638.808 1908.24,-627.552 1923.21,-617.759"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1925.27,-620.593 1931.72,-612.19 1921.44,-614.735 1925.27,-620.593"/>
-</g>
-<!-- 23->31 -->
-<g id="edge55" class="edge"><title>23->31</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1766.32,-647.996C1717.81,-638.018 1655.86,-624.873 1601,-612 1600.9,-611.976 1600.8,-611.953 1600.7,-611.929"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1601.67,-608.563 1591.13,-609.633 1600.04,-615.37 1601.67,-608.563"/>
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-<!-- 24->14 -->
-<g id="edge31" class="edge"><title>24->14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1631.68,-722.094C1649.83,-713.907 1668.55,-701.707 1679,-684 1691.28,-663.202 1677.19,-638.237 1662.11,-620.048"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1664.44,-617.398 1655.21,-612.207 1659.19,-622.025 1664.44,-617.398"/>
+<!-- 24 -->
+<g id="node25" class="node">
+<title>24</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M1292.5,-324C1292.5,-324 1233.5,-324 1233.5,-324 1227.5,-324 1221.5,-318 1221.5,-312 1221.5,-312 1221.5,-300 1221.5,-300 1221.5,-294 1227.5,-288 1233.5,-288 1233.5,-288 1292.5,-288 1292.5,-288 1298.5,-288 1304.5,-294 1304.5,-300 1304.5,-300 1304.5,-312 1304.5,-312 1304.5,-318 1298.5,-324 1292.5,-324"/>
+<text text-anchor="middle" x="1263" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
+<text text-anchor="middle" x="1263" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: plus</text>
+</g>
+<!-- 24->2 -->
+<g id="edge24" class="edge">
+<title>24->2</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1304.8785,-288.5708C1328.8198,-278.6068 1359.0413,-266.0291 1384.4348,-255.4607"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1386.0201,-258.592 1393.9076,-251.5182 1383.3304,-252.1293 1386.0201,-258.592"/>
</g>
<!-- 25 -->
-<g id="node26" class="node"><title>25</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1658,-684C1658,-684 1508,-684 1508,-684 1502,-684 1496,-678 1496,-672 1496,-672 1496,-660 1496,-660 1496,-654 1502,-648 1508,-648 1508,-648 1658,-648 1658,-648 1664,-648 1670,-654 1670,-660 1670,-660 1670,-672 1670,-672 1670,-678 1664,-684 1658,-684"/>
-<text text-anchor="middle" x="1583" y="-669" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
-<text text-anchor="middle" x="1583" y="-658" font-family="sans" font-size="10.00">seqmode: single_end</text>
+<g id="node26" class="node">
+<title>25</title>
+<path fill="none" stroke="#56d8d0" stroke-width="2" d="M2154.5,-689C2154.5,-689 2053.5,-689 2053.5,-689 2047.5,-689 2041.5,-683 2041.5,-677 2041.5,-677 2041.5,-660 2041.5,-660 2041.5,-654 2047.5,-648 2053.5,-648 2053.5,-648 2154.5,-648 2154.5,-648 2160.5,-648 2166.5,-654 2166.5,-660 2166.5,-660 2166.5,-677 2166.5,-677 2166.5,-683 2160.5,-689 2154.5,-689"/>
+<text text-anchor="middle" x="2104" y="-677" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
+<text text-anchor="middle" x="2104" y="-666" font-family="sans" font-size="10.00" fill="#000000">index_size: 75</text>
+<text text-anchor="middle" x="2104" y="-655" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
+</g>
+<!-- 25->2 -->
+<g id="edge25" class="edge">
+<title>25->2</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2041.3603,-663.1749C1955.9554,-655.0738 1808.1874,-637.8165 1761,-612 1713.7893,-586.1707 1680,-575.8145 1680,-522 1680,-522 1680,-522 1680,-378 1680,-337.1184 1689.966,-316.8493 1661,-288 1607.232,-234.4487 1566.3755,-270.1408 1487.9182,-251.8789"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1488.7166,-248.4705 1478.1604,-249.3748 1486.9765,-255.2508 1488.7166,-248.4705"/>
+</g>
+<!-- 25->3 -->
+<g id="edge27" class="edge">
+<title>25->3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2104,-647.6361C2104,-619.2216 2104,-566.7639 2104,-522 2104,-522 2104,-522 2104,-378 2104,-337.1184 2113.4398,-317.3681 2085,-288 2040.309,-241.8502 2005.6944,-268.5447 1938.8459,-251.9029"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1939.7647,-248.5257 1929.195,-249.2549 1937.9125,-255.2762 1939.7647,-248.5257"/>
+</g>
+<!-- 25->4 -->
+<g id="edge29" class="edge">
+<title>25->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2041.1233,-658.0445C1931.7457,-638.0605 1718,-590.2734 1718,-522 1718,-522 1718,-522 1718,-378 1718,-336.6022 1722.1904,-318.3163 1694,-288 1694,-288 1635.0939,-267.6094 1589.6766,-251.8881"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1590.8106,-248.5769 1580.2158,-248.6132 1588.5208,-255.1918 1590.8106,-248.5769"/>
+</g>
+<!-- 25->5 -->
+<g id="edge31" class="edge">
+<title>25->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2144.8701,-647.9116C2186.1931,-623.8599 2244,-579.8715 2244,-522 2244,-522 2244,-522 2244,-378 2244,-337.1184 2254.1361,-316.6775 2225,-288 2167.517,-231.4217 2124.1462,-270.8194 2040.9493,-251.8734"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2041.7008,-248.4536 2031.1496,-249.4141 2039.9969,-255.243 2041.7008,-248.4536"/>
+</g>
+<!-- 25->6 -->
+<g id="edge33" class="edge">
+<title>25->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2166.8375,-663.0924C2249.3908,-652.1517 2384,-619.3815 2384,-522 2384,-522 2384,-522 2384,-378 2384,-337.1184 2394.5931,-316.2056 2365,-288 2294.5983,-220.8992 2242.6159,-273.301 2142.9204,-251.8357"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2143.6581,-248.4137 2133.1213,-249.5214 2142.049,-255.2263 2143.6581,-248.4137"/>
+</g>
+<!-- 25->7 -->
+<g id="edge35" class="edge">
+<title>25->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2166.8146,-662.0602C2252.1164,-652.6611 2399.6214,-633.9005 2449,-612 2507.6913,-585.9692 2562,-586.2049 2562,-522 2562,-522 2562,-522 2562,-378 2562,-335.3959 2560.6703,-316.4974 2529,-288 2516.8301,-277.0493 2425.8533,-256.7992 2366.2078,-244.4497"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2366.6922,-240.9762 2356.192,-242.3891 2365.2815,-247.8326 2366.6922,-240.9762"/>
+</g>
+<!-- 25->8 -->
+<g id="edge37" class="edge">
+<title>25->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2166.8782,-659.9276C2284.0442,-642.181 2524,-596.7154 2524,-522 2524,-522 2524,-522 2524,-378 2524,-337.1184 2534.7671,-316.0219 2505,-288 2465.412,-250.7329 2316.2892,-262.7847 2263,-252 2257.1696,-250.82 2251.0981,-249.4598 2245.0748,-248.0266"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2245.5803,-244.5469 2235.0345,-245.5646 2243.9132,-251.3455 2245.5803,-244.5469"/>
+</g>
+<!-- 25->9 -->
+<g id="edge39" class="edge">
+<title>25->9</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2166.6966,-664.3304C2264.0804,-657.0782 2446.5765,-640.1625 2505,-612 2557.3918,-586.745 2600,-580.1611 2600,-522 2600,-522 2600,-522 2600,-378 2600,-333.4756 2586.9729,-319.986 2556,-288 2541.8754,-273.4134 2522.9504,-261.9134 2505.2388,-253.3421"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2506.6648,-250.1455 2496.1191,-249.1259 2503.7273,-256.4993 2506.6648,-250.1455"/>
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-<!-- 24->25 -->
-<g id="edge49" class="edge"><title>24->25</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1583,-719.697C1583,-711.983 1583,-702.712 1583,-694.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1586.5,-694.104 1583,-684.104 1579.5,-694.104 1586.5,-694.104"/>
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-<!-- 32 -->
-<g id="node33" class="node"><title>32</title>
-<path fill="none" stroke="#56d86b" stroke-width="2" d="M1449,-612C1449,-612 1361,-612 1361,-612 1355,-612 1349,-606 1349,-600 1349,-600 1349,-588 1349,-588 1349,-582 1355,-576 1361,-576 1361,-576 1449,-576 1449,-576 1455,-576 1461,-582 1461,-588 1461,-588 1461,-600 1461,-600 1461,-606 1455,-612 1449,-612"/>
-<text text-anchor="middle" x="1405" y="-591.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
-</g>
-<!-- 24->32 -->
-<g id="edge57" class="edge"><title>24->32</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1534.42,-734.18C1466.9,-729.131 1350.04,-715.914 1324,-684 1313.88,-671.604 1316.39,-662.074 1324,-648 1330.82,-635.391 1342.09,-625.3 1354.08,-617.45"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1356.14,-620.294 1362.89,-612.126 1352.52,-614.303 1356.14,-620.294"/>
+<!-- 42 -->
+<g id="node43" class="node">
+<title>42</title>
+<path fill="none" stroke="#97d856" stroke-width="2" d="M923.5,-612C923.5,-612 834.5,-612 834.5,-612 828.5,-612 822.5,-606 822.5,-600 822.5,-600 822.5,-588 822.5,-588 822.5,-582 828.5,-576 834.5,-576 834.5,-576 923.5,-576 923.5,-576 929.5,-576 935.5,-582 935.5,-588 935.5,-588 935.5,-600 935.5,-600 935.5,-606 929.5,-612 923.5,-612"/>
+<text text-anchor="middle" x="879" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
</g>
-<!-- 25->14 -->
-<g id="edge32" class="edge"><title>25->14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1596.35,-647.697C1602.76,-639.389 1610.56,-629.277 1617.61,-620.141"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1620.47,-622.16 1623.81,-612.104 1614.93,-617.884 1620.47,-622.16"/>
+<!-- 25->42 -->
+<g id="edge79" class="edge">
+<title>25->42</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2041.1437,-664.6773C1831.9638,-651.9558 1160.438,-611.116 945.7009,-598.0565"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="945.7162,-594.5511 935.5222,-597.4375 945.2912,-601.5381 945.7162,-594.5511"/>
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-<!-- 25->32 -->
-<g id="edge58" class="edge"><title>25->32</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1539.46,-647.876C1514.8,-638.179 1483.78,-625.98 1457.75,-615.743"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1458.99,-612.471 1448.4,-612.068 1456.43,-618.985 1458.99,-612.471"/>
+<!-- 44 -->
+<g id="node45" class="node">
+<title>44</title>
+<path fill="none" stroke="#56d873" stroke-width="2" d="M1385.5,-612C1385.5,-612 1312.5,-612 1312.5,-612 1306.5,-612 1300.5,-606 1300.5,-600 1300.5,-600 1300.5,-588 1300.5,-588 1300.5,-582 1306.5,-576 1312.5,-576 1312.5,-576 1385.5,-576 1385.5,-576 1391.5,-576 1397.5,-582 1397.5,-588 1397.5,-588 1397.5,-600 1397.5,-600 1397.5,-606 1391.5,-612 1385.5,-612"/>
+<text text-anchor="middle" x="1349" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+</g>
+<!-- 25->44 -->
+<g id="edge82" class="edge">
+<title>25->44</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2041.2506,-662.3082C1897.814,-648.1545 1547.5911,-613.5961 1407.9188,-599.8138"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1408.1304,-596.3178 1397.835,-598.8188 1407.443,-603.284 1408.1304,-596.3178"/>
+</g>
+<!-- 63 -->
+<g id="node64" class="node">
+<title>63</title>
+<path fill="none" stroke="#d8d356" stroke-width="2" d="M1640,-396C1640,-396 1560,-396 1560,-396 1554,-396 1548,-390 1548,-384 1548,-384 1548,-372 1548,-372 1548,-366 1554,-360 1560,-360 1560,-360 1640,-360 1640,-360 1646,-360 1652,-366 1652,-372 1652,-372 1652,-384 1652,-384 1652,-390 1646,-396 1640,-396"/>
+<text text-anchor="middle" x="1600" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">generate_alfa_index</text>
+</g>
+<!-- 25->63 -->
+<g id="edge111" class="edge">
+<title>25->63</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2041.2327,-664.2134C1926.9104,-655.8563 1693.8957,-636.0786 1666,-612 1605.2719,-559.5817 1598.3365,-456.0229 1598.7931,-406.148"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1602.2938,-406.1458 1598.9947,-396.0777 1595.2952,-406.0056 1602.2938,-406.1458"/>
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<!-- 26 -->
-<g id="node27" class="node"><title>26</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M1905.5,-396C1905.5,-396 1824.5,-396 1824.5,-396 1818.5,-396 1812.5,-390 1812.5,-384 1812.5,-384 1812.5,-372 1812.5,-372 1812.5,-366 1818.5,-360 1824.5,-360 1824.5,-360 1905.5,-360 1905.5,-360 1911.5,-360 1917.5,-366 1917.5,-372 1917.5,-372 1917.5,-384 1917.5,-384 1917.5,-390 1911.5,-396 1905.5,-396"/>
-<text text-anchor="middle" x="1865" y="-375.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
-</g>
-<!-- 26->15 -->
-<g id="edge33" class="edge"><title>26->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1834.91,-359.876C1818.68,-350.639 1798.46,-339.131 1781.03,-329.212"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1782.63,-326.094 1772.2,-324.19 1779.16,-332.178 1782.63,-326.094"/>
+<g id="node27" class="node">
+<title>26</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M1567.5,-324C1567.5,-324 1508.5,-324 1508.5,-324 1502.5,-324 1496.5,-318 1496.5,-312 1496.5,-312 1496.5,-300 1496.5,-300 1496.5,-294 1502.5,-288 1508.5,-288 1508.5,-288 1567.5,-288 1567.5,-288 1573.5,-288 1579.5,-294 1579.5,-300 1579.5,-300 1579.5,-312 1579.5,-312 1579.5,-318 1573.5,-324 1567.5,-324"/>
+<text text-anchor="middle" x="1538" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
+<text text-anchor="middle" x="1538" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: plus</text>
+</g>
+<!-- 26->3 -->
+<g id="edge26" class="edge">
+<title>26->3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1579.5478,-290.5942C1582.7249,-289.6444 1585.9006,-288.7651 1589,-288 1693.5493,-262.1921 1726.379,-277.6181 1834.8587,-252.006"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1835.9983,-255.3312 1844.8915,-249.5726 1834.3483,-248.5284 1835.9983,-255.3312"/>
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<!-- 27 -->
-<g id="node28" class="node"><title>27</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M1782.5,-396C1782.5,-396 1701.5,-396 1701.5,-396 1695.5,-396 1689.5,-390 1689.5,-384 1689.5,-384 1689.5,-372 1689.5,-372 1689.5,-366 1695.5,-360 1701.5,-360 1701.5,-360 1782.5,-360 1782.5,-360 1788.5,-360 1794.5,-366 1794.5,-372 1794.5,-372 1794.5,-384 1794.5,-384 1794.5,-390 1788.5,-396 1782.5,-396"/>
-<text text-anchor="middle" x="1742" y="-375.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
-</g>
-<!-- 27->15 -->
-<g id="edge34" class="edge"><title>27->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1742,-359.697C1742,-351.983 1742,-342.712 1742,-334.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1745.5,-334.104 1742,-324.104 1738.5,-334.104 1745.5,-334.104"/>
+<g id="node28" class="node">
+<title>27</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M1393.5,-324C1393.5,-324 1334.5,-324 1334.5,-324 1328.5,-324 1322.5,-318 1322.5,-312 1322.5,-312 1322.5,-300 1322.5,-300 1322.5,-294 1328.5,-288 1334.5,-288 1334.5,-288 1393.5,-288 1393.5,-288 1399.5,-288 1405.5,-294 1405.5,-300 1405.5,-300 1405.5,-312 1405.5,-312 1405.5,-318 1399.5,-324 1393.5,-324"/>
+<text text-anchor="middle" x="1364" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
+<text text-anchor="middle" x="1364" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: minus</text>
+</g>
+<!-- 27->4 -->
+<g id="edge28" class="edge">
+<title>27->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1405.6773,-288.7542C1429.9435,-278.713 1460.7364,-265.9711 1486.5101,-255.3062"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1487.8552,-258.5374 1495.7571,-251.4798 1485.1787,-252.0693 1487.8552,-258.5374"/>
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<!-- 28 -->
-<g id="node29" class="node"><title>28</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M1400,-905C1400,-905 1132,-905 1132,-905 1126,-905 1120,-899 1120,-893 1120,-893 1120,-881 1120,-881 1120,-875 1126,-869 1132,-869 1132,-869 1400,-869 1400,-869 1406,-869 1412,-875 1412,-881 1412,-881 1412,-893 1412,-893 1412,-899 1406,-905 1400,-905"/>
-<text text-anchor="middle" x="1266" y="-890" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1266" y="-879" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
-</g>
-<!-- 28->16 -->
-<g id="edge35" class="edge"><title>28->16</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1266,-868.819C1266,-860.422 1266,-850.116 1266,-840.686"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1269.5,-840.558 1266,-830.558 1262.5,-840.558 1269.5,-840.558"/>
+<g id="node29" class="node">
+<title>28</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M1817.5,-324C1817.5,-324 1758.5,-324 1758.5,-324 1752.5,-324 1746.5,-318 1746.5,-312 1746.5,-312 1746.5,-300 1746.5,-300 1746.5,-294 1752.5,-288 1758.5,-288 1758.5,-288 1817.5,-288 1817.5,-288 1823.5,-288 1829.5,-294 1829.5,-300 1829.5,-300 1829.5,-312 1829.5,-312 1829.5,-318 1823.5,-324 1817.5,-324"/>
+<text text-anchor="middle" x="1788" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
+<text text-anchor="middle" x="1788" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: minus</text>
+</g>
+<!-- 28->5 -->
+<g id="edge30" class="edge">
+<title>28->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1829.6473,-291.0816C1860.8353,-279.9098 1903.6984,-264.5558 1937.115,-252.5857"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1938.4806,-255.8144 1946.7145,-249.147 1936.1199,-249.2244 1938.4806,-255.8144"/>
</g>
<!-- 29 -->
-<g id="node30" class="node"><title>29</title>
-<path fill="none" stroke="#56d88a" stroke-width="2" d="M1106.5,-612C1106.5,-612 1005.5,-612 1005.5,-612 999.5,-612 993.5,-606 993.5,-600 993.5,-600 993.5,-588 993.5,-588 993.5,-582 999.5,-576 1005.5,-576 1005.5,-576 1106.5,-576 1106.5,-576 1112.5,-576 1118.5,-582 1118.5,-588 1118.5,-588 1118.5,-600 1118.5,-600 1118.5,-606 1112.5,-612 1106.5,-612"/>
-<text text-anchor="middle" x="1056" y="-597" font-family="sans" font-size="10.00">extract_transcriptome</text>
-<text text-anchor="middle" x="1056" y="-586" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
-</g>
-<!-- 29->17 -->
-<g id="edge36" class="edge"><title>29->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1078.25,-575.697C1089.58,-566.881 1103.53,-556.032 1115.82,-546.474"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1118.26,-549.007 1124.01,-540.104 1113.97,-543.481 1118.26,-549.007"/>
-</g>
-<!-- 40 -->
-<g id="node41" class="node"><title>40</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M1061.5,-540C1061.5,-540 890.5,-540 890.5,-540 884.5,-540 878.5,-534 878.5,-528 878.5,-528 878.5,-516 878.5,-516 878.5,-510 884.5,-504 890.5,-504 890.5,-504 1061.5,-504 1061.5,-504 1067.5,-504 1073.5,-510 1073.5,-516 1073.5,-516 1073.5,-528 1073.5,-528 1073.5,-534 1067.5,-540 1061.5,-540"/>
-<text text-anchor="middle" x="976" y="-519.5" font-family="sans" font-size="10.00">concatenate_transcriptome_and_genome</text>
-</g>
-<!-- 29->40 -->
-<g id="edge70" class="edge"><title>29->40</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1036.22,-575.697C1026.25,-566.965 1013.99,-556.24 1003.14,-546.75"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1005.38,-544.055 995.548,-540.104 1000.77,-549.323 1005.38,-544.055"/>
+<g id="node30" class="node">
+<title>29</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M2063.5,-324C2063.5,-324 2004.5,-324 2004.5,-324 1998.5,-324 1992.5,-318 1992.5,-312 1992.5,-312 1992.5,-300 1992.5,-300 1992.5,-294 1998.5,-288 2004.5,-288 2004.5,-288 2063.5,-288 2063.5,-288 2069.5,-288 2075.5,-294 2075.5,-300 2075.5,-300 2075.5,-312 2075.5,-312 2075.5,-318 2069.5,-324 2063.5,-324"/>
+<text text-anchor="middle" x="2034" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
+<text text-anchor="middle" x="2034" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: plus</text>
+</g>
+<!-- 29->6 -->
+<g id="edge32" class="edge">
+<title>29->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2048.3835,-287.8314C2054.9486,-279.5386 2062.8507,-269.557 2070.0578,-260.4533"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2072.9599,-262.4262 2076.4228,-252.4133 2067.4716,-258.0813 2072.9599,-262.4262"/>
</g>
<!-- 30 -->
-<g id="node31" class="node"><title>30</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M847,-905C847,-905 567,-905 567,-905 561,-905 555,-899 555,-893 555,-893 555,-881 555,-881 555,-875 561,-869 567,-869 567,-869 847,-869 847,-869 853,-869 859,-875 859,-881 859,-881 859,-893 859,-893 859,-899 853,-905 847,-905"/>
-<text text-anchor="middle" x="707" y="-890" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="707" y="-879" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
-</g>
-<!-- 30->18 -->
-<g id="edge37" class="edge"><title>30->18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M707,-868.819C707,-860.422 707,-850.116 707,-840.686"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="710.5,-840.558 707,-830.558 703.5,-840.558 710.5,-840.558"/>
-</g>
-<!-- 31->19 -->
-<g id="edge38" class="edge"><title>31->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1504.91,-575.876C1488.68,-566.639 1468.46,-555.131 1451.03,-545.212"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1452.63,-542.094 1442.2,-540.19 1449.16,-548.178 1452.63,-542.094"/>
-</g>
-<!-- 32->19 -->
-<g id="edge39" class="edge"><title>32->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1406.73,-575.697C1407.5,-567.983 1408.43,-558.712 1409.29,-550.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1412.78,-550.403 1410.29,-540.104 1405.81,-549.706 1412.78,-550.403"/>
+<g id="node31" class="node">
+<title>30</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M2343.5,-324C2343.5,-324 2284.5,-324 2284.5,-324 2278.5,-324 2272.5,-318 2272.5,-312 2272.5,-312 2272.5,-300 2272.5,-300 2272.5,-294 2278.5,-288 2284.5,-288 2284.5,-288 2343.5,-288 2343.5,-288 2349.5,-288 2355.5,-294 2355.5,-300 2355.5,-300 2355.5,-312 2355.5,-312 2355.5,-318 2349.5,-324 2343.5,-324"/>
+<text text-anchor="middle" x="2314" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
+<text text-anchor="middle" x="2314" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: plus</text>
+</g>
+<!-- 30->7 -->
+<g id="edge34" class="edge">
+<title>30->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2314,-287.8314C2314,-280.131 2314,-270.9743 2314,-262.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2317.5001,-262.4132 2314,-252.4133 2310.5001,-262.4133 2317.5001,-262.4132"/>
</g>
-<!-- 33 -->
-<g id="node34" class="node"><title>33</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M979.5,-468C979.5,-468 894.5,-468 894.5,-468 888.5,-468 882.5,-462 882.5,-456 882.5,-456 882.5,-444 882.5,-444 882.5,-438 888.5,-432 894.5,-432 894.5,-432 979.5,-432 979.5,-432 985.5,-432 991.5,-438 991.5,-444 991.5,-444 991.5,-456 991.5,-456 991.5,-462 985.5,-468 979.5,-468"/>
-<text text-anchor="middle" x="937" y="-447.5" font-family="sans" font-size="10.00">create_index_salmon</text>
+<!-- 31 -->
+<g id="node32" class="node">
+<title>31</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M2203.5,-324C2203.5,-324 2144.5,-324 2144.5,-324 2138.5,-324 2132.5,-318 2132.5,-312 2132.5,-312 2132.5,-300 2132.5,-300 2132.5,-294 2138.5,-288 2144.5,-288 2144.5,-288 2203.5,-288 2203.5,-288 2209.5,-288 2215.5,-294 2215.5,-300 2215.5,-300 2215.5,-312 2215.5,-312 2215.5,-318 2209.5,-324 2203.5,-324"/>
+<text text-anchor="middle" x="2174" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
+<text text-anchor="middle" x="2174" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: minus</text>
+</g>
+<!-- 31->8 -->
+<g id="edge36" class="edge">
+<title>31->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2178.7945,-287.8314C2180.8489,-280.0463 2183.296,-270.7729 2185.5756,-262.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2188.9735,-262.9753 2188.1409,-252.4133 2182.2052,-261.1892 2188.9735,-262.9753"/>
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-<!-- 33->20 -->
-<g id="edge41" class="edge"><title>33->20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M966.355,-431.876C982.045,-422.724 1001.56,-411.342 1018.45,-401.485"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1020.66,-404.252 1027.53,-396.19 1017.13,-398.205 1020.66,-404.252"/>
+<!-- 32 -->
+<g id="node33" class="node">
+<title>32</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M2483.5,-324C2483.5,-324 2424.5,-324 2424.5,-324 2418.5,-324 2412.5,-318 2412.5,-312 2412.5,-312 2412.5,-300 2412.5,-300 2412.5,-294 2418.5,-288 2424.5,-288 2424.5,-288 2483.5,-288 2483.5,-288 2489.5,-288 2495.5,-294 2495.5,-300 2495.5,-300 2495.5,-312 2495.5,-312 2495.5,-318 2489.5,-324 2483.5,-324"/>
+<text text-anchor="middle" x="2454" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
+<text text-anchor="middle" x="2454" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: minus</text>
+</g>
+<!-- 32->9 -->
+<g id="edge38" class="edge">
+<title>32->9</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2454,-287.8314C2454,-280.131 2454,-270.9743 2454,-262.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2457.5001,-262.4132 2454,-252.4133 2450.5001,-262.4133 2457.5001,-262.4132"/>
</g>
-<!-- 33->21 -->
-<g id="edge43" class="edge"><title>33->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M929.09,-431.697C925.447,-423.728 921.046,-414.1 917.006,-405.264"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="920.16,-403.744 912.819,-396.104 913.794,-406.654 920.16,-403.744"/>
+<!-- 33 -->
+<g id="node34" class="node">
+<title>33</title>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M280,-838C280,-838 12,-838 12,-838 6,-838 0,-832 0,-826 0,-826 0,-809 0,-809 0,-803 6,-797 12,-797 12,-797 280,-797 280,-797 286,-797 292,-803 292,-809 292,-809 292,-826 292,-826 292,-832 286,-838 280,-838"/>
+<text text-anchor="middle" x="146" y="-826" font-family="sans" font-size="10.00" fill="#000000">start</text>
+<text text-anchor="middle" x="146" y="-815" font-family="sans" font-size="10.00" fill="#000000">mate: fq1</text>
+<text text-anchor="middle" x="146" y="-804" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+</g>
+<!-- 33->10 -->
+<g id="edge40" class="edge">
+<title>33->10</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M136.1255,-796.8743C116.7494,-756.4018 73.7511,-666.5877 52.0567,-621.2726"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="55.1181,-619.5617 47.643,-612.0534 48.8043,-622.5844 55.1181,-619.5617"/>
+</g>
+<!-- 52 -->
+<g id="node53" class="node">
+<title>52</title>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M569,-761C569,-761 443,-761 443,-761 437,-761 431,-755 431,-749 431,-749 431,-737 431,-737 431,-731 437,-725 443,-725 443,-725 569,-725 569,-725 575,-725 581,-731 581,-737 581,-737 581,-749 581,-749 581,-755 575,-761 569,-761"/>
+<text text-anchor="middle" x="506" y="-740.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
+</g>
+<!-- 33->52 -->
+<g id="edge93" class="edge">
+<title>33->52</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M245.3246,-796.9453C300.4611,-785.5351 368.3312,-771.4898 420.9952,-760.5913"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="421.8975,-763.9788 430.9807,-758.5248 420.4789,-757.124 421.8975,-763.9788"/>
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<!-- 34 -->
-<g id="node35" class="node"><title>34</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M1828.5,-833C1828.5,-833 1727.5,-833 1727.5,-833 1721.5,-833 1715.5,-827 1715.5,-821 1715.5,-821 1715.5,-804 1715.5,-804 1715.5,-798 1721.5,-792 1727.5,-792 1727.5,-792 1828.5,-792 1828.5,-792 1834.5,-792 1840.5,-798 1840.5,-804 1840.5,-804 1840.5,-821 1840.5,-821 1840.5,-827 1834.5,-833 1828.5,-833"/>
-<text text-anchor="middle" x="1778" y="-821" font-family="sans" font-size="10.00">create_index_star</text>
-<text text-anchor="middle" x="1778" y="-810" font-family="sans" font-size="10.00">index_size: 75</text>
-<text text-anchor="middle" x="1778" y="-799" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
-</g>
-<!-- 34->22 -->
-<g id="edge44" class="edge"><title>34->22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1778,-791.689C1778,-783.907 1778,-774.842 1778,-766.447"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1781.5,-766.319 1778,-756.319 1774.5,-766.32 1781.5,-766.319"/>
-</g>
-<!-- 34->24 -->
-<g id="edge47" class="edge"><title>34->24</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1725.49,-791.976C1698.54,-781.959 1665.73,-769.76 1638.39,-759.594"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1639.56,-756.294 1628.96,-756.09 1637.12,-762.855 1639.56,-756.294"/>
-</g>
-<!-- 43 -->
-<g id="node44" class="node"><title>43</title>
-<path fill="none" stroke="#5682d8" stroke-width="2" d="M2054,-540C2054,-540 1974,-540 1974,-540 1968,-540 1962,-534 1962,-528 1962,-528 1962,-516 1962,-516 1962,-510 1968,-504 1974,-504 1974,-504 2054,-504 2054,-504 2060,-504 2066,-510 2066,-516 2066,-516 2066,-528 2066,-528 2066,-534 2060,-540 2054,-540"/>
-<text text-anchor="middle" x="2014" y="-519.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
-</g>
-<!-- 34->43 -->
-<g id="edge72" class="edge"><title>34->43</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1821.52,-791.833C1863.92,-770.678 1927.59,-733.322 1967,-684 1998.41,-644.69 2008.83,-585.094 2012.29,-550.508"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="2015.8,-550.48 2013.18,-540.215 2008.83,-549.874 2015.8,-550.48"/>
+<g id="node35" class="node">
+<title>34</title>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M605,-838C605,-838 325,-838 325,-838 319,-838 313,-832 313,-826 313,-826 313,-809 313,-809 313,-803 319,-797 325,-797 325,-797 605,-797 605,-797 611,-797 617,-803 617,-809 617,-809 617,-826 617,-826 617,-832 611,-838 605,-838"/>
+<text text-anchor="middle" x="465" y="-826" font-family="sans" font-size="10.00" fill="#000000">start</text>
+<text text-anchor="middle" x="465" y="-815" font-family="sans" font-size="10.00" fill="#000000">mate: fq1</text>
+<text text-anchor="middle" x="465" y="-804" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+</g>
+<!-- 34->11 -->
+<g id="edge41" class="edge">
+<title>34->11</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M445.8117,-796.7822C421.0352,-770.0308 377.9109,-723.469 350.9944,-694.407"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="353.224,-691.6635 343.8611,-686.7051 348.0883,-696.4201 353.224,-691.6635"/>
+</g>
+<!-- 54 -->
+<g id="node55" class="node">
+<title>54</title>
+<path fill="none" stroke="#56d8c1" stroke-width="2" d="M751,-761C751,-761 641,-761 641,-761 635,-761 629,-755 629,-749 629,-749 629,-737 629,-737 629,-731 635,-725 641,-725 641,-725 751,-725 751,-725 757,-725 763,-731 763,-737 763,-737 763,-749 763,-749 763,-755 757,-761 751,-761"/>
+<text text-anchor="middle" x="696" y="-740.5" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
+</g>
+<!-- 34->54 -->
+<g id="edge95" class="edge">
+<title>34->54</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M528.7333,-796.9453C560.3206,-786.7581 598.4211,-774.4703 630.2754,-764.1969"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="631.5037,-767.4784 639.9466,-761.0778 629.355,-760.8163 631.5037,-767.4784"/>
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<!-- 35 -->
-<g id="node36" class="node"><title>35</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M2029,-468C2029,-468 1999,-468 1999,-468 1993,-468 1987,-462 1987,-456 1987,-456 1987,-444 1987,-444 1987,-438 1993,-432 1999,-432 1999,-432 2029,-432 2029,-432 2035,-432 2041,-438 2041,-444 2041,-444 2041,-456 2041,-456 2041,-462 2035,-468 2029,-468"/>
-<text text-anchor="middle" x="2014" y="-447.5" font-family="sans" font-size="10.00">alfa_qc</text>
-</g>
-<!-- 35->26 -->
-<g id="edge50" class="edge"><title>35->26</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1986.67,-436.161C1965.44,-426.186 1935.53,-412.133 1910.67,-400.456"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1911.96,-397.196 1901.42,-396.111 1908.99,-403.531 1911.96,-397.196"/>
+<g id="node36" class="node">
+<title>35</title>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1042,-838C1042,-838 774,-838 774,-838 768,-838 762,-832 762,-826 762,-826 762,-809 762,-809 762,-803 768,-797 774,-797 774,-797 1042,-797 1042,-797 1048,-797 1054,-803 1054,-809 1054,-809 1054,-826 1054,-826 1054,-832 1048,-838 1042,-838"/>
+<text text-anchor="middle" x="908" y="-826" font-family="sans" font-size="10.00" fill="#000000">start</text>
+<text text-anchor="middle" x="908" y="-815" font-family="sans" font-size="10.00" fill="#000000">mate: fq2</text>
+<text text-anchor="middle" x="908" y="-804" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+</g>
+<!-- 35->12 -->
+<g id="edge42" class="edge">
+<title>35->12</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M952.972,-796.9453C978.5944,-785.2345 1010.29,-770.7478 1034.382,-759.7364"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1035.9021,-762.89 1043.5422,-755.5497 1032.9922,-756.5234 1035.9021,-762.89"/>
+</g>
+<!-- 35->52 -->
+<g id="edge94" class="edge">
+<title>35->52</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M797.3539,-796.9947C732.1855,-784.9175 651.0154,-769.8747 590.9142,-758.7366"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="591.5494,-755.2948 581.079,-756.9139 590.2738,-762.1776 591.5494,-755.2948"/>
</g>
<!-- 36 -->
-<g id="node37" class="node"><title>36</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1854,-468C1854,-468 1824,-468 1824,-468 1818,-468 1812,-462 1812,-456 1812,-456 1812,-444 1812,-444 1812,-438 1818,-432 1824,-432 1824,-432 1854,-432 1854,-432 1860,-432 1866,-438 1866,-444 1866,-444 1866,-456 1866,-456 1866,-462 1860,-468 1854,-468"/>
-<text text-anchor="middle" x="1839" y="-447.5" font-family="sans" font-size="10.00">alfa_qc</text>
+<g id="node37" class="node">
+<title>36</title>
+<path fill="none" stroke="#56d892" stroke-width="2" d="M562,-686.5C562,-686.5 450,-686.5 450,-686.5 444,-686.5 438,-680.5 438,-674.5 438,-674.5 438,-662.5 438,-662.5 438,-656.5 444,-650.5 450,-650.5 450,-650.5 562,-650.5 562,-650.5 568,-650.5 574,-656.5 574,-662.5 574,-662.5 574,-674.5 574,-674.5 574,-680.5 568,-686.5 562,-686.5"/>
+<text text-anchor="middle" x="506" y="-666" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
</g>
-<!-- 36->26 -->
-<g id="edge51" class="edge"><title>36->26</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1845.43,-431.697C1848.36,-423.813 1851.89,-414.304 1855.14,-405.546"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1858.45,-406.697 1858.65,-396.104 1851.88,-404.26 1858.45,-406.697"/>
+<!-- 36->13 -->
+<g id="edge43" class="edge">
+<title>36->13</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M441.1153,-650.4283C383.0432,-629.8279 307,-589.8908 307,-522 307,-522 307,-522 307,-378 307,-335.6562 288.4068,-289.6118 274.6094,-261.273"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="277.5809,-259.3907 269.9675,-252.0228 271.3245,-262.5304 277.5809,-259.3907"/>
</g>
-<!-- 37 -->
-<g id="node38" class="node"><title>37</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1926,-468C1926,-468 1896,-468 1896,-468 1890,-468 1884,-462 1884,-456 1884,-456 1884,-444 1884,-444 1884,-438 1890,-432 1896,-432 1896,-432 1926,-432 1926,-432 1932,-432 1938,-438 1938,-444 1938,-444 1938,-456 1938,-456 1938,-462 1932,-468 1926,-468"/>
-<text text-anchor="middle" x="1911" y="-447.5" font-family="sans" font-size="10.00">alfa_qc</text>
+<!-- 40 -->
+<g id="node41" class="node">
+<title>40</title>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M644.5,-252C644.5,-252 541.5,-252 541.5,-252 535.5,-252 529.5,-246 529.5,-240 529.5,-240 529.5,-228 529.5,-228 529.5,-222 535.5,-216 541.5,-216 541.5,-216 644.5,-216 644.5,-216 650.5,-216 656.5,-222 656.5,-228 656.5,-228 656.5,-240 656.5,-240 656.5,-246 650.5,-252 644.5,-252"/>
+<text text-anchor="middle" x="593" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
+</g>
+<!-- 36->40 -->
+<g id="edge75" class="edge">
+<title>36->40</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M506,-650.4571C506,-622.8072 506,-568.2899 506,-522 506,-522 506,-522 506,-450 506,-374.906 517.7221,-353.7497 554,-288 559.1957,-278.5834 565.7633,-268.882 572.0204,-260.3455"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="574.8955,-262.3458 578.1117,-252.2509 569.3022,-258.1367 574.8955,-262.3458"/>
+</g>
+<!-- 36->42 -->
+<g id="edge80" class="edge">
+<title>36->42</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M574.4139,-654.8356C642.1298,-641.3105 745.1289,-620.7383 812.257,-607.3307"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="813.181,-610.7154 822.3018,-605.3244 811.8099,-603.8509 813.181,-610.7154"/>
</g>
-<!-- 37->27 -->
-<g id="edge52" class="edge"><title>37->27</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1883.96,-436.009C1880.95,-434.629 1877.92,-433.268 1875,-432 1849.34,-420.843 1820.54,-409.251 1796.31,-399.763"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1797.51,-396.475 1786.92,-396.102 1794.97,-402.997 1797.51,-396.475"/>
+<!-- 37 -->
+<g id="node38" class="node">
+<title>37</title>
+<path fill="none" stroke="#afd856" stroke-width="2" d="M457,-324C457,-324 373,-324 373,-324 367,-324 361,-318 361,-312 361,-312 361,-300 361,-300 361,-294 367,-288 373,-288 373,-288 457,-288 457,-288 463,-288 469,-294 469,-300 469,-300 469,-312 469,-312 469,-318 463,-324 457,-324"/>
+<text text-anchor="middle" x="415" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
+</g>
+<!-- 37->13 -->
+<g id="edge44" class="edge">
+<title>37->13</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M375.887,-287.8314C355.2488,-278.2446 329.7516,-266.4008 307.9327,-256.2655"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="309.3756,-253.0766 298.8318,-252.038 306.4266,-259.4251 309.3756,-253.0766"/>
+</g>
+<!-- 37->14 -->
+<g id="edge46" class="edge">
+<title>37->14</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M420.2992,-287.8314C422.5698,-280.0463 425.2746,-270.7729 427.794,-262.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="431.1894,-262.9933 430.6295,-252.4133 424.4694,-261.0332 431.1894,-262.9933"/>
</g>
<!-- 38 -->
-<g id="node39" class="node"><title>38</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1757,-468C1757,-468 1727,-468 1727,-468 1721,-468 1715,-462 1715,-456 1715,-456 1715,-444 1715,-444 1715,-438 1721,-432 1727,-432 1727,-432 1757,-432 1757,-432 1763,-432 1769,-438 1769,-444 1769,-444 1769,-456 1769,-456 1769,-462 1763,-468 1757,-468"/>
-<text text-anchor="middle" x="1742" y="-447.5" font-family="sans" font-size="10.00">alfa_qc</text>
+<g id="node39" class="node">
+<title>38</title>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M759,-686.5C759,-686.5 663,-686.5 663,-686.5 657,-686.5 651,-680.5 651,-674.5 651,-674.5 651,-662.5 651,-662.5 651,-656.5 657,-650.5 663,-650.5 663,-650.5 759,-650.5 759,-650.5 765,-650.5 771,-656.5 771,-662.5 771,-662.5 771,-674.5 771,-674.5 771,-680.5 765,-686.5 759,-686.5"/>
+<text text-anchor="middle" x="711" y="-666" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
</g>
-<!-- 38->27 -->
-<g id="edge53" class="edge"><title>38->27</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1742,-431.697C1742,-423.983 1742,-414.712 1742,-406.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1745.5,-406.104 1742,-396.104 1738.5,-406.104 1745.5,-406.104"/>
+<!-- 38->14 -->
+<g id="edge45" class="edge">
+<title>38->14</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M706.2344,-650.1441C699.4975,-622.5387 688,-568.5995 688,-522 688,-522 688,-522 688,-450 688,-409.0242 695.6837,-390.2097 668,-360 632.1028,-320.8273 601.1597,-348.476 554,-324 520.0424,-306.376 485.7772,-278.9165 462.9864,-258.9614"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="465.2241,-256.2677 455.4228,-252.2444 460.5759,-261.5017 465.2241,-256.2677"/>
</g>
-<!-- 39 -->
-<g id="node40" class="node"><title>39</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M1465.5,-684C1465.5,-684 1344.5,-684 1344.5,-684 1338.5,-684 1332.5,-678 1332.5,-672 1332.5,-672 1332.5,-660 1332.5,-660 1332.5,-654 1338.5,-648 1344.5,-648 1344.5,-648 1465.5,-648 1465.5,-648 1471.5,-648 1477.5,-654 1477.5,-660 1477.5,-660 1477.5,-672 1477.5,-672 1477.5,-678 1471.5,-684 1465.5,-684"/>
-<text text-anchor="middle" x="1405" y="-663.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+<!-- 41 -->
+<g id="node42" class="node">
+<title>41</title>
+<path fill="none" stroke="#68d856" stroke-width="2" d="M773.5,-252C773.5,-252 686.5,-252 686.5,-252 680.5,-252 674.5,-246 674.5,-240 674.5,-240 674.5,-228 674.5,-228 674.5,-222 680.5,-216 686.5,-216 686.5,-216 773.5,-216 773.5,-216 779.5,-216 785.5,-222 785.5,-228 785.5,-228 785.5,-240 785.5,-240 785.5,-246 779.5,-252 773.5,-252"/>
+<text text-anchor="middle" x="730" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
+</g>
+<!-- 38->41 -->
+<g id="edge77" class="edge">
+<title>38->41</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M714.108,-650.0609C718.5016,-622.3494 726,-568.2763 726,-522 726,-522 726,-522 726,-378 726,-337.8605 727.5722,-291.4516 728.7453,-262.4112"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="732.2521,-262.3179 729.1712,-252.1809 725.2581,-262.0266 732.2521,-262.3179"/>
+</g>
+<!-- 38->44 -->
+<g id="edge83" class="edge">
+<title>38->44</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M771.0215,-661.4912C893.0937,-647.2367 1168.9639,-615.023 1290.0933,-600.8786"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1290.756,-604.3251 1300.2825,-599.6888 1289.944,-597.3723 1290.756,-604.3251"/>
</g>
-<!-- 39->31 -->
-<g id="edge56" class="edge"><title>39->31</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1436.8,-647.876C1454.11,-638.554 1475.72,-626.919 1494.26,-616.939"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1495.93,-620.012 1503.08,-612.19 1492.61,-613.849 1495.93,-620.012"/>
+<!-- 39 -->
+<g id="node40" class="node">
+<title>39</title>
+<path fill="none" stroke="#56d882" stroke-width="2" d="M1120,-396C1120,-396 1044,-396 1044,-396 1038,-396 1032,-390 1032,-384 1032,-384 1032,-372 1032,-372 1032,-366 1038,-360 1044,-360 1044,-360 1120,-360 1120,-360 1126,-360 1132,-366 1132,-372 1132,-372 1132,-384 1132,-384 1132,-390 1126,-396 1120,-396"/>
+<text text-anchor="middle" x="1082" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">merge_TIN_scores</text>
+</g>
+<!-- 39->15 -->
+<g id="edge47" class="edge">
+<title>39->15</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1082,-359.9555C1082,-322.3938 1082,-235.5541 1082,-190.4103"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1085.5001,-190.145 1082,-180.1451 1078.5001,-190.1451 1085.5001,-190.145"/>
+</g>
+<!-- 40->16 -->
+<g id="edge48" class="edge">
+<title>40->16</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M632.3654,-215.8314C653.1367,-206.2446 678.7983,-194.4008 700.7581,-184.2655"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="702.3048,-187.4065 709.9177,-180.038 699.3714,-181.0508 702.3048,-187.4065"/>
+</g>
+<!-- 40->17 -->
+<g id="edge50" class="edge">
+<title>40->17</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M656.5811,-218.0084C659.4248,-217.3235 662.2412,-216.6513 665,-216 680.7453,-212.283 761.2088,-194.4393 825.2937,-180.2665"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="826.4175,-183.6026 835.4259,-178.0261 824.9061,-176.7677 826.4175,-183.6026"/>
+</g>
+<!-- 40->18 -->
+<g id="edge52" class="edge">
+<title>40->18</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M547.3261,-215.8314C522.9032,-206.1162 492.6534,-194.0831 466.9516,-183.8592"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="467.931,-180.4821 457.3455,-180.038 465.3437,-186.9864 467.931,-180.4821"/>
+</g>
+<!-- 40->19 -->
+<g id="edge54" class="edge">
+<title>40->19</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M590.9813,-215.8314C590.1257,-208.131 589.1083,-198.9743 588.1574,-190.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="591.6289,-189.9656 587.0459,-180.4133 584.6717,-190.7386 591.6289,-189.9656"/>
+</g>
+<!-- 41->16 -->
+<g id="edge49" class="edge">
+<title>41->16</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M734.7945,-215.8314C736.8489,-208.0463 739.296,-198.7729 741.5756,-190.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="744.9735,-190.9753 744.1409,-180.4133 738.2052,-189.1892 744.9735,-190.9753"/>
+</g>
+<!-- 41->17 -->
+<g id="edge51" class="edge">
+<title>41->17</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M774.9169,-215.8314C798.935,-206.1162 828.6834,-194.0831 853.9592,-183.8592"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="855.4482,-187.0325 863.4061,-180.038 852.8233,-180.5432 855.4482,-187.0325"/>
+</g>
+<!-- 41->18 -->
+<g id="edge53" class="edge">
+<title>41->18</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M674.3881,-218.3641C671.2168,-217.5459 668.0708,-216.7522 665,-216 648.7917,-212.0298 566.1324,-194.4694 499.641,-180.4364"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="500.0472,-176.9451 489.54,-178.3055 498.6022,-183.7944 500.0472,-176.9451"/>
+</g>
+<!-- 41->19 -->
+<g id="edge55" class="edge">
+<title>41->19</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M693.4104,-215.8314C674.2761,-206.3302 650.6771,-194.6121 630.3878,-184.5374"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="631.8397,-181.3506 621.3265,-180.038 628.7265,-187.6203 631.8397,-181.3506"/>
+</g>
+<!-- 42->20 -->
+<g id="edge56" class="edge">
+<title>42->20</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M824.7405,-575.9128C808.4149,-567.642 792.3643,-556.0115 783,-540 774.9225,-526.1886 774.0299,-517.2491 783,-504 804.5513,-472.168 848.2339,-459.0988 880.0914,-453.734"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="881.0203,-457.1341 890.3929,-452.194 879.9853,-450.211 881.0203,-457.1341"/>
</g>
-<!-- 39->32 -->
-<g id="edge59" class="edge"><title>39->32</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1405,-647.697C1405,-639.983 1405,-630.712 1405,-622.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1408.5,-622.104 1405,-612.104 1401.5,-622.104 1408.5,-622.104"/>
+<!-- 43 -->
+<g id="node44" class="node">
+<title>43</title>
+<path fill="none" stroke="#ced856" stroke-width="2" d="M954,-540C954,-540 804,-540 804,-540 798,-540 792,-534 792,-528 792,-528 792,-516 792,-516 792,-510 798,-504 804,-504 804,-504 954,-504 954,-504 960,-504 966,-510 966,-516 966,-516 966,-528 966,-528 966,-534 960,-540 954,-540"/>
+<text text-anchor="middle" x="879" y="-525" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="879" y="-514" font-family="sans" font-size="10.00" fill="#000000">seqmode: pe</text>
+</g>
+<!-- 42->43 -->
+<g id="edge81" class="edge">
+<title>42->43</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M879,-575.8314C879,-568.131 879,-558.9743 879,-550.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="882.5001,-550.4132 879,-540.4133 875.5001,-550.4133 882.5001,-550.4132"/>
+</g>
+<!-- 55 -->
+<g id="node56" class="node">
+<title>55</title>
+<path fill="none" stroke="#d87556" stroke-width="2" d="M1064,-468C1064,-468 976,-468 976,-468 970,-468 964,-462 964,-456 964,-456 964,-444 964,-444 964,-438 970,-432 976,-432 976,-432 1064,-432 1064,-432 1070,-432 1076,-438 1076,-444 1076,-444 1076,-456 1076,-456 1076,-462 1070,-468 1064,-468"/>
+<text text-anchor="middle" x="1020" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
+</g>
+<!-- 42->55 -->
+<g id="edge96" class="edge">
+<title>42->55</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M923.3895,-575.9625C941.0874,-567.1234 960.625,-555.0933 975,-540 991.9283,-522.2258 1003.8302,-496.8505 1011.1237,-477.5724"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1014.4325,-478.714 1014.5198,-468.1195 1007.8447,-476.3472 1014.4325,-478.714"/>
+</g>
+<!-- 43->20 -->
+<g id="edge57" class="edge">
+<title>43->20</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M888.8413,-503.8314C893.1957,-495.7925 898.4098,-486.1666 903.2169,-477.2918"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="906.3408,-478.8732 908.0261,-468.4133 900.1857,-475.5392 906.3408,-478.8732"/>
+</g>
+<!-- 43->55 -->
+<g id="edge97" class="edge">
+<title>43->55</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M914.5803,-503.8314C933.0325,-494.4089 955.7545,-482.8062 975.373,-472.7883"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="977.1168,-475.8278 984.4311,-468.1628 973.9333,-469.5935 977.1168,-475.8278"/>
+</g>
+<!-- 44->21 -->
+<g id="edge58" class="edge">
+<title>44->21</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1397.8953,-576.4505C1415.1813,-567.9496 1433.2316,-556.0316 1445,-540 1458.0158,-522.2691 1462.5259,-497.5652 1463.9152,-478.5241"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1467.4206,-478.4934 1464.4068,-468.3363 1460.4288,-478.1559 1467.4206,-478.4934"/>
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-<!-- 40->33 -->
-<g id="edge60" class="edge"><title>40->33</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M966.36,-503.697C961.873,-495.644 956.441,-485.894 951.476,-476.982"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="954.454,-475.137 946.53,-468.104 948.339,-478.544 954.454,-475.137"/>
+<!-- 45 -->
+<g id="node46" class="node">
+<title>45</title>
+<path fill="none" stroke="#ced856" stroke-width="2" d="M1424,-540C1424,-540 1274,-540 1274,-540 1268,-540 1262,-534 1262,-528 1262,-528 1262,-516 1262,-516 1262,-510 1268,-504 1274,-504 1274,-504 1424,-504 1424,-504 1430,-504 1436,-510 1436,-516 1436,-516 1436,-528 1436,-528 1436,-534 1430,-540 1424,-540"/>
+<text text-anchor="middle" x="1349" y="-525" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="1349" y="-514" font-family="sans" font-size="10.00" fill="#000000">seqmode: se</text>
+</g>
+<!-- 44->45 -->
+<g id="edge84" class="edge">
+<title>44->45</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1349,-575.8314C1349,-568.131 1349,-558.9743 1349,-550.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1352.5001,-550.4132 1349,-540.4133 1345.5001,-550.4133 1352.5001,-550.4132"/>
+</g>
+<!-- 56 -->
+<g id="node57" class="node">
+<title>56</title>
+<path fill="none" stroke="#d87556" stroke-width="2" d="M1194,-468C1194,-468 1106,-468 1106,-468 1100,-468 1094,-462 1094,-456 1094,-456 1094,-444 1094,-444 1094,-438 1100,-432 1106,-432 1106,-432 1194,-432 1194,-432 1200,-432 1206,-438 1206,-444 1206,-444 1206,-456 1206,-456 1206,-462 1200,-468 1194,-468"/>
+<text text-anchor="middle" x="1150" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
+</g>
+<!-- 44->56 -->
+<g id="edge99" class="edge">
+<title>44->56</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1312.8301,-575.9289C1294.3752,-566.1489 1271.8951,-553.3548 1253,-540 1224.9717,-520.19 1195.7599,-494.0605 1175.6354,-475.062"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1178.0432,-472.5218 1168.3888,-468.1578 1173.2146,-477.5898 1178.0432,-472.5218"/>
+</g>
+<!-- 45->21 -->
+<g id="edge59" class="edge">
+<title>45->21</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1378.0194,-503.8314C1393.0654,-494.4112 1411.5922,-482.8118 1427.5905,-472.7955"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1429.5615,-475.6909 1436.18,-467.4177 1425.8469,-469.7578 1429.5615,-475.6909"/>
+</g>
+<!-- 45->56 -->
+<g id="edge100" class="edge">
+<title>45->56</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1299.0408,-503.9243C1271.8363,-494.0815 1237.9983,-481.8386 1209.4438,-471.5073"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1210.5741,-468.1943 1199.9798,-468.0831 1208.1924,-474.7767 1210.5741,-468.1943"/>
</g>
-<!-- 41 -->
-<g id="node42" class="node"><title>41</title>
-<path fill="none" stroke="#d8ac56" stroke-width="2" d="M848.5,-540C848.5,-540 747.5,-540 747.5,-540 741.5,-540 735.5,-534 735.5,-528 735.5,-528 735.5,-516 735.5,-516 735.5,-510 741.5,-504 747.5,-504 747.5,-504 848.5,-504 848.5,-504 854.5,-504 860.5,-510 860.5,-516 860.5,-516 860.5,-528 860.5,-528 860.5,-534 854.5,-540 848.5,-540"/>
-<text text-anchor="middle" x="798" y="-525" font-family="sans" font-size="10.00">extract_decoys_salmon</text>
-<text text-anchor="middle" x="798" y="-514" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
-</g>
-<!-- 41->33 -->
-<g id="edge61" class="edge"><title>41->33</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M832.003,-503.876C850.598,-494.512 873.827,-482.814 893.706,-472.803"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="895.509,-475.814 902.866,-468.19 892.36,-469.562 895.509,-475.814"/>
-</g>
-<!-- 42->35 -->
-<g id="edge62" class="edge"><title>42->35</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M2115.98,-503.876C2096.07,-493.557 2070.71,-480.403 2050.25,-469.797"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="2051.73,-466.619 2041.24,-465.123 2048.5,-472.833 2051.73,-466.619"/>
-</g>
-<!-- 43->35 -->
-<g id="edge63" class="edge"><title>43->35</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M2014,-503.697C2014,-495.983 2014,-486.712 2014,-478.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="2017.5,-478.104 2014,-468.104 2010.5,-478.104 2017.5,-478.104"/>
-</g>
-<!-- 43->36 -->
-<g id="edge65" class="edge"><title>43->36</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1966.67,-503.982C1941.84,-494.818 1910.78,-482.99 1875.56,-468.1"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1876.6,-464.736 1866.03,-464.035 1873.85,-471.176 1876.6,-464.736"/>
-</g>
-<!-- 43->37 -->
-<g id="edge67" class="edge"><title>43->37</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1988.8,-503.876C1975.59,-494.893 1959.21,-483.763 1944.89,-474.034"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1946.53,-470.916 1936.29,-468.19 1942.6,-476.705 1946.53,-470.916"/>
-</g>
-<!-- 43->38 -->
-<g id="edge69" class="edge"><title>43->38</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1961.79,-506.316C1958.82,-505.522 1955.87,-504.745 1953,-504 1886.63,-486.794 1869.37,-485.206 1803,-468 1795.22,-465.982 1786.9,-463.73 1779,-461.543"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1779.85,-458.145 1769.27,-458.828 1777.96,-464.887 1779.85,-458.145"/>
-</g>
-<!-- 44->36 -->
-<g id="edge64" class="edge"><title>44->36</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1757.42,-503.876C1771.41,-494.808 1788.78,-483.552 1803.89,-473.759"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1805.99,-476.566 1812.48,-468.19 1802.18,-470.692 1805.99,-476.566"/>
-</g>
-<!-- 45->37 -->
-<g id="edge66" class="edge"><title>45->37</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1886.91,-503.697C1890.55,-495.728 1894.95,-486.1 1898.99,-477.264"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1902.21,-478.654 1903.18,-468.104 1895.84,-475.744 1902.21,-478.654"/>
-</g>
-<!-- 46->38 -->
-<g id="edge68" class="edge"><title>46->38</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1621.9,-503.876C1647.49,-492.607 1680.77,-477.957 1705.8,-466.936"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1707.22,-470.138 1714.96,-462.905 1704.4,-463.731 1707.22,-470.138"/>
+<!-- 46 -->
+<g id="node47" class="node">
+<title>46</title>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1691.5,-252C1691.5,-252 1610.5,-252 1610.5,-252 1604.5,-252 1598.5,-246 1598.5,-240 1598.5,-240 1598.5,-228 1598.5,-228 1598.5,-222 1604.5,-216 1610.5,-216 1610.5,-216 1691.5,-216 1691.5,-216 1697.5,-216 1703.5,-222 1703.5,-228 1703.5,-228 1703.5,-240 1703.5,-240 1703.5,-246 1697.5,-252 1691.5,-252"/>
+<text text-anchor="middle" x="1651" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
+</g>
+<!-- 46->22 -->
+<g id="edge60" class="edge">
+<title>46->22</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1651,-215.8314C1651,-208.131 1651,-198.9743 1651,-190.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1654.5001,-190.4132 1651,-180.4133 1647.5001,-190.4133 1654.5001,-190.4132"/>
+</g>
+<!-- 47 -->
+<g id="node48" class="node">
+<title>47</title>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1814.5,-252C1814.5,-252 1733.5,-252 1733.5,-252 1727.5,-252 1721.5,-246 1721.5,-240 1721.5,-240 1721.5,-228 1721.5,-228 1721.5,-222 1727.5,-216 1733.5,-216 1733.5,-216 1814.5,-216 1814.5,-216 1820.5,-216 1826.5,-222 1826.5,-228 1826.5,-228 1826.5,-240 1826.5,-240 1826.5,-246 1820.5,-252 1814.5,-252"/>
+<text text-anchor="middle" x="1774" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
+</g>
+<!-- 47->22 -->
+<g id="edge61" class="edge">
+<title>47->22</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1742.9619,-215.8314C1727.2295,-206.6221 1707.9389,-195.3301 1691.0956,-185.4706"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1692.4265,-182.1941 1682.0282,-180.1628 1688.8902,-188.2352 1692.4265,-182.1941"/>
+</g>
+<!-- 48->24 -->
+<g id="edge62" class="edge">
+<title>48->24</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1293.654,-359.8314C1289.0763,-351.7925 1283.5948,-342.1666 1278.5412,-333.2918"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1281.4752,-331.3712 1273.4853,-324.4133 1275.3923,-334.8351 1281.4752,-331.3712"/>
+</g>
+<!-- 48->27 -->
+<g id="edge64" class="edge">
+<title>48->27</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1319.1405,-359.8314C1326.1217,-351.454 1334.5391,-341.3531 1342.1876,-332.1749"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1344.9425,-334.3362 1348.6556,-324.4133 1339.5649,-329.8548 1344.9425,-334.3362"/>
+</g>
+<!-- 58 -->
+<g id="node59" class="node">
+<title>58</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M1466,-324C1466,-324 1436,-324 1436,-324 1430,-324 1424,-318 1424,-312 1424,-312 1424,-300 1424,-300 1424,-294 1430,-288 1436,-288 1436,-288 1466,-288 1466,-288 1472,-288 1478,-294 1478,-300 1478,-300 1478,-312 1478,-312 1478,-318 1472,-324 1466,-324"/>
+<text text-anchor="middle" x="1451" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
+</g>
+<!-- 48->58 -->
+<g id="edge103" class="edge">
+<title>48->58</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1341.3026,-359.9776C1360.8441,-350.508 1385.3678,-338.5805 1414.6491,-324.1529"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1416.4691,-327.1578 1423.8889,-319.595 1413.3723,-320.8801 1416.4691,-327.1578"/>
+</g>
+<!-- 49->26 -->
+<g id="edge63" class="edge">
+<title>49->26</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1483.421,-359.8314C1492.1529,-351.219 1502.7317,-340.7851 1512.2423,-331.4048"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1514.923,-333.6769 1519.5849,-324.1628 1510.0075,-328.6931 1514.923,-333.6769"/>
+</g>
+<!-- 49->28 -->
+<g id="edge65" class="edge">
+<title>49->28</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1530.3489,-362.0103C1533.2712,-361.325 1536.1652,-360.652 1539,-360 1606.9559,-344.369 1685.6371,-327.5125 1736.0669,-316.8669"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1737.0116,-320.2447 1746.0747,-314.7575 1735.5678,-313.3952 1737.0116,-320.2447"/>
+</g>
+<!-- 60 -->
+<g id="node61" class="node">
+<title>60</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M1640,-324C1640,-324 1610,-324 1610,-324 1604,-324 1598,-318 1598,-312 1598,-312 1598,-300 1598,-300 1598,-294 1604,-288 1610,-288 1610,-288 1640,-288 1640,-288 1646,-288 1652,-294 1652,-300 1652,-300 1652,-312 1652,-312 1652,-318 1646,-324 1640,-324"/>
+<text text-anchor="middle" x="1625" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
+</g>
+<!-- 49->60 -->
+<g id="edge107" class="edge">
+<title>49->60</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1508.004,-359.9355C1529.9206,-350.5777 1557.1387,-338.7269 1588.8769,-323.9605"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1590.3725,-327.125 1597.948,-319.718 1587.4069,-320.7842 1590.3725,-327.125"/>
+</g>
+<!-- 50->29 -->
+<g id="edge66" class="edge">
+<title>50->29</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1906.1505,-359.8314C1929.4718,-350.0119 1958.4169,-337.8245 1982.865,-327.5305"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1984.4814,-330.6476 1992.3396,-323.5412 1981.765,-324.1961 1984.4814,-330.6476"/>
+</g>
+<!-- 50->31 -->
+<g id="edge68" class="edge">
+<title>50->31</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1928.3576,-362.0475C1931.2775,-361.3521 1934.1687,-360.6669 1937,-360 2000.8505,-344.9611 2074.541,-328.2761 2122.5806,-317.4887"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2123.4384,-320.8833 2132.4296,-315.279 2121.906,-314.0531 2123.4384,-320.8833"/>
+</g>
+<!-- 59 -->
+<g id="node60" class="node">
+<title>59</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M1890,-324C1890,-324 1860,-324 1860,-324 1854,-324 1848,-318 1848,-312 1848,-312 1848,-300 1848,-300 1848,-294 1854,-288 1860,-288 1860,-288 1890,-288 1890,-288 1896,-288 1902,-294 1902,-300 1902,-300 1902,-312 1902,-312 1902,-318 1896,-324 1890,-324"/>
+<text text-anchor="middle" x="1875" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
+</g>
+<!-- 50->59 -->
+<g id="edge105" class="edge">
+<title>50->59</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1866.0281,-359.8314C1867.3115,-352.131 1868.8376,-342.9743 1870.2639,-334.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1873.7394,-334.8526 1871.9311,-324.4133 1866.8347,-333.7018 1873.7394,-334.8526"/>
+</g>
+<!-- 51->30 -->
+<g id="edge67" class="edge">
+<title>51->30</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2076.0011,-362.5542C2131.7544,-349.3059 2211.0118,-330.4724 2262.472,-318.2443"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2263.4583,-321.6075 2272.3782,-315.8903 2261.8399,-314.7971 2263.4583,-321.6075"/>
+</g>
+<!-- 51->32 -->
+<g id="edge69" class="edge">
+<title>51->32</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2076.0749,-369.0321C2147.2046,-359.0065 2264.4549,-341.8255 2365,-324 2377.1267,-321.8501 2390.1406,-319.336 2402.3709,-316.8802"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2403.3191,-320.2592 2412.4233,-314.8404 2401.9269,-313.399 2403.3191,-320.2592"/>
+</g>
+<!-- 61 -->
+<g id="node62" class="node">
+<title>61</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M1962,-324C1962,-324 1932,-324 1932,-324 1926,-324 1920,-318 1920,-312 1920,-312 1920,-300 1920,-300 1920,-294 1926,-288 1932,-288 1932,-288 1962,-288 1962,-288 1968,-288 1974,-294 1974,-300 1974,-300 1974,-312 1974,-312 1974,-318 1968,-324 1962,-324"/>
+<text text-anchor="middle" x="1947" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
+</g>
+<!-- 51->61 -->
+<g id="edge109" class="edge">
+<title>51->61</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1994.8501,-359.8314C1987.3283,-351.3694 1978.2435,-341.1489 1970.0196,-331.8971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1972.627,-329.5621 1963.3673,-324.4133 1967.3951,-334.2127 1972.627,-329.5621"/>
+</g>
+<!-- 52->36 -->
+<g id="edge70" class="edge">
+<title>52->36</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M506,-724.9656C506,-716.5178 506,-706.2542 506,-696.8064"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="509.5001,-696.6265 506,-686.6265 502.5001,-696.6265 509.5001,-696.6265"/>
+</g>
+<!-- 53 -->
+<g id="node54" class="node">
+<title>53</title>
+<path fill="none" stroke="#78d856" stroke-width="2" d="M647.5,-396C647.5,-396 546.5,-396 546.5,-396 540.5,-396 534.5,-390 534.5,-384 534.5,-384 534.5,-372 534.5,-372 534.5,-366 540.5,-360 546.5,-360 546.5,-360 647.5,-360 647.5,-360 653.5,-360 659.5,-366 659.5,-372 659.5,-372 659.5,-384 659.5,-384 659.5,-390 653.5,-396 647.5,-396"/>
+<text text-anchor="middle" x="597" y="-381" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
+<text text-anchor="middle" x="597" y="-370" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
+</g>
+<!-- 53->37 -->
+<g id="edge71" class="edge">
+<title>53->37</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M551.0737,-359.8314C526.4077,-350.0734 495.8309,-337.977 469.914,-327.7242"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="471.1824,-324.4621 460.596,-324.038 468.6073,-330.9713 471.1824,-324.4621"/>
+</g>
+<!-- 57 -->
+<g id="node58" class="node">
+<title>57</title>
+<path fill="none" stroke="#59d856" stroke-width="2" d="M660.5,-324C660.5,-324 575.5,-324 575.5,-324 569.5,-324 563.5,-318 563.5,-312 563.5,-312 563.5,-300 563.5,-300 563.5,-294 569.5,-288 575.5,-288 575.5,-288 660.5,-288 660.5,-288 666.5,-288 672.5,-294 672.5,-300 672.5,-300 672.5,-312 672.5,-312 672.5,-318 666.5,-324 660.5,-324"/>
+<text text-anchor="middle" x="618" y="-309" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
+<text text-anchor="middle" x="618" y="-298" font-family="sans" font-size="10.00" fill="#000000">kmer: 31</text>
+</g>
+<!-- 53->57 -->
+<g id="edge102" class="edge">
+<title>53->57</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M602.2992,-359.8314C604.5698,-352.0463 607.2746,-342.7729 609.794,-334.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="613.1894,-334.9933 612.6295,-324.4133 606.4694,-333.0332 613.1894,-334.9933"/>
+</g>
+<!-- 54->38 -->
+<g id="edge72" class="edge">
+<title>54->38</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M699.6311,-724.9656C701.3503,-716.427 703.443,-706.0333 705.362,-696.502"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="708.8076,-697.1206 707.3504,-686.6265 701.9453,-695.7389 708.8076,-697.1206"/>
+</g>
+<!-- 55->39 -->
+<g id="edge73" class="edge">
+<title>55->39</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1035.6452,-431.8314C1042.8591,-423.454 1051.557,-413.3531 1059.4605,-404.1749"/>
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+</g>
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+<title>56->39</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1132.8407,-431.8314C1124.8489,-423.3694 1115.1962,-413.1489 1106.4584,-403.8971"/>
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+</g>
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+</g>
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+<g id="edge85" class="edge">
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+</g>
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+</g>
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+</g>
+<!-- 62 -->
+<g id="node63" class="node">
+<title>62</title>
+<path fill="none" stroke="#9fd856" stroke-width="2" d="M1155.5,-540C1155.5,-540 1034.5,-540 1034.5,-540 1028.5,-540 1022.5,-534 1022.5,-528 1022.5,-528 1022.5,-516 1022.5,-516 1022.5,-510 1028.5,-504 1034.5,-504 1034.5,-504 1155.5,-504 1155.5,-504 1161.5,-504 1167.5,-510 1167.5,-516 1167.5,-516 1167.5,-528 1167.5,-528 1167.5,-534 1161.5,-540 1155.5,-540"/>
+<text text-anchor="middle" x="1095" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
+</g>
+<!-- 62->55 -->
+<g id="edge98" class="edge">
+<title>62->55</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1076.0743,-503.8314C1067.0143,-495.1337 1056.0191,-484.5783 1046.1735,-475.1265"/>
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+</g>
+<!-- 62->56 -->
+<g id="edge101" class="edge">
+<title>62->56</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1108.8788,-503.8314C1115.2136,-495.5386 1122.8384,-485.557 1129.7926,-476.4533"/>
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+</g>
+<!-- 63->58 -->
+<g id="edge104" class="edge">
+<title>63->58</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1562.3953,-359.9098C1540.649,-349.4383 1512.7706,-335.9967 1488,-324 1487.6986,-323.854 1487.3959,-323.7074 1487.092,-323.5601"/>
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+</g>
+<!-- 63->59 -->
+<g id="edge106" class="edge">
+<title>63->59</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1652.3057,-369.9324C1699.2181,-361.8642 1769.8102,-347.6631 1838.1559,-323.8804"/>
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+</g>
+<!-- 63->60 -->
+<g id="edge108" class="edge">
+<title>63->60</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1606.3086,-359.8314C1609.0117,-352.0463 1612.2316,-342.7729 1615.231,-334.1347"/>
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+</g>
+<!-- 63->61 -->
+<g id="edge110" class="edge">
+<title>63->61</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1652.0265,-373.6397C1712.6331,-367.5383 1815.5165,-354.005 1910.1182,-323.7841"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1911.4145,-327.0428 1919.8337,-320.6111 1909.2412,-320.3887 1911.4145,-327.0428"/>
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diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index c2634ec020a62da06b89678a633a96fd9ce35a55..a91d8306daf880d3ccd8fe80c97270d1d64b70c7 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -1,443 +1,541 @@
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<title>snakemake_dag</title>
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+<polygon fill="#ffffff" stroke="transparent" points="-4,4 -4,-832 1145,-832 1145,4 -4,4"/>
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-<text text-anchor="middle" x="472" y="-15.5" font-family="sans" font-size="10.00">finish</text>
+<g id="node1" class="node">
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+<path fill="none" stroke="#d8a456" stroke-width="2" d="M850,-36C850,-36 820,-36 820,-36 814,-36 808,-30 808,-24 808,-24 808,-12 808,-12 808,-6 814,0 820,0 820,0 850,0 850,0 856,0 862,-6 862,-12 862,-12 862,-24 862,-24 862,-30 856,-36 850,-36"/>
+<text text-anchor="middle" x="835" y="-15.5" font-family="sans" font-size="10.00" fill="#000000">finish</text>
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-<text text-anchor="middle" x="472" y="-87.5" font-family="sans" font-size="10.00">MULTIQC_report</text>
+<g id="node2" class="node">
+<title>1</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M524,-108C524,-108 470,-108 470,-108 464,-108 458,-102 458,-96 458,-96 458,-84 458,-84 458,-78 464,-72 470,-72 470,-72 524,-72 524,-72 530,-72 536,-78 536,-84 536,-84 536,-96 536,-96 536,-102 530,-108 524,-108"/>
+<text text-anchor="middle" x="497" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">multiqc_report</text>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="475.5,-46.1043 472,-36.1043 468.5,-46.1044 475.5,-46.1043"/>
+<g id="edge1" class="edge">
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M536.1031,-81.6703C601.7824,-67.6795 733.3738,-39.6482 797.7732,-25.93"/>
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-<text text-anchor="middle" x="472" y="-159.5" font-family="sans" font-size="10.00">prepare_MultiQC_config</text>
+<g id="node3" class="node">
+<title>2</title>
+<path fill="none" stroke="#56d892" stroke-width="2" d="M1057,-252C1057,-252 997,-252 997,-252 991,-252 985,-246 985,-240 985,-240 985,-228 985,-228 985,-222 991,-216 997,-216 997,-216 1057,-216 1057,-216 1063,-216 1069,-222 1069,-228 1069,-228 1069,-240 1069,-240 1069,-246 1063,-252 1057,-252"/>
+<text text-anchor="middle" x="1027" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="475.5,-118.104 472,-108.104 468.5,-118.104 475.5,-118.104"/>
+<!-- 2->0 -->
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+<title>2->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1010.9604,-215.9555C976.937,-177.6791 897.4281,-88.2316 858.0038,-43.8793"/>
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-<text text-anchor="middle" x="472" y="-231.5" font-family="sans" font-size="10.00">prepare_files_for_report</text>
+<g id="node4" class="node">
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+<text text-anchor="middle" x="1114" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="475.5,-190.104 472,-180.104 468.5,-190.104 475.5,-190.104"/>
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+<title>3->1</title>
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-<text text-anchor="middle" x="72" y="-303.5" font-family="sans" font-size="10.00">pe_fastqc</text>
+<g id="node5" class="node">
+<title>4</title>
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+<text text-anchor="middle" x="251" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="402.53,-243.219 412.206,-238.905 401.951,-236.243 402.53,-243.219"/>
+<!-- 4->1 -->
+<g id="edge9" class="edge">
+<title>4->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M209.46,-575.9345C193.9343,-567.2099 177.5318,-555.2708 167,-540 143.7899,-506.3459 148,-490.8816 148,-450 148,-450 148,-450 148,-234 148,-169.8895 351.7892,-119.674 447.9171,-99.5534"/>
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-<text text-anchor="middle" x="147" y="-303.5" font-family="sans" font-size="10.00">fastqc</text>
+<g id="node6" class="node">
+<title>5</title>
+<path fill="none" stroke="#afd856" stroke-width="2" d="M138,-612C138,-612 12,-612 12,-612 6,-612 0,-606 0,-600 0,-600 0,-588 0,-588 0,-582 6,-576 12,-576 12,-576 138,-576 138,-576 144,-576 150,-582 150,-588 150,-588 150,-600 150,-600 150,-606 144,-612 138,-612"/>
+<text text-anchor="middle" x="75" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
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+<title>5->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M78.7296,-575.9053C84.0019,-548.7046 93,-495.6021 93,-450 93,-450 93,-450 93,-234 93,-173.5425 140.5601,-170.2947 195,-144 238.8594,-122.8157 374.1983,-104.3382 447.9158,-95.5129"/>
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+<path fill="none" stroke="#d8d356" stroke-width="2" d="M541.5,-252C541.5,-252 476.5,-252 476.5,-252 470.5,-252 464.5,-246 464.5,-240 464.5,-240 464.5,-228 464.5,-228 464.5,-222 470.5,-216 476.5,-216 476.5,-216 541.5,-216 541.5,-216 547.5,-216 553.5,-222 553.5,-228 553.5,-228 553.5,-240 553.5,-240 553.5,-246 547.5,-252 541.5,-252"/>
+<text text-anchor="middle" x="509" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">plot_TIN_scores</text>
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+<g id="edge4" class="edge">
+<title>6->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M494.7641,-215.6423C487.9461,-205.6872 480.5138,-192.8222 477,-180 471.2889,-159.1601 477.1631,-135.2715 483.9919,-117.3451"/>
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-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M463,-756C463,-756 337,-756 337,-756 331,-756 325,-750 325,-744 325,-744 325,-732 325,-732 325,-726 331,-720 337,-720 337,-720 463,-720 463,-720 469,-720 475,-726 475,-732 475,-732 475,-744 475,-744 475,-750 469,-756 463,-756"/>
-<text text-anchor="middle" x="400" y="-735.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
+<g id="node8" class="node">
+<title>7</title>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M300,-540C300,-540 188,-540 188,-540 182,-540 176,-534 176,-528 176,-528 176,-516 176,-516 176,-510 182,-504 188,-504 188,-504 300,-504 300,-504 306,-504 312,-510 312,-516 312,-516 312,-528 312,-528 312,-534 306,-540 300,-540"/>
+<text text-anchor="middle" x="244" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
</g>
-<!-- 7->3 -->
-<g id="edge7" class="edge"><title>7->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M324.739,-723.249C297.831,-715.35 268.805,-703.05 247,-684 213.62,-654.838 202,-639.324 202,-595 202,-595 202,-595 202,-377 202,-286.466 322.383,-253.524 402.383,-241.628"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="402.999,-245.076 412.413,-240.214 402.022,-238.144 402.999,-245.076"/>
+<!-- 7->1 -->
+<g id="edge6" class="edge">
+<title>7->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M257.9817,-503.5693C276.5421,-477.217 307,-426.5724 307,-378 307,-378 307,-378 307,-234 307,-163.3284 391.525,-122.8695 447.8213,-103.76"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="449.218,-106.9856 457.6319,-100.5469 447.0392,-100.3333 449.218,-106.9856"/>
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<!-- 8 -->
-<g id="node9" class="node"><title>8</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M685.5,-396C685.5,-396 620.5,-396 620.5,-396 614.5,-396 608.5,-390 608.5,-384 608.5,-384 608.5,-372 608.5,-372 608.5,-366 614.5,-360 620.5,-360 620.5,-360 685.5,-360 685.5,-360 691.5,-360 697.5,-366 697.5,-372 697.5,-372 697.5,-384 697.5,-384 697.5,-390 691.5,-396 685.5,-396"/>
-<text text-anchor="middle" x="653" y="-375.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
+<g id="node9" class="node">
+<title>8</title>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M473.5,-540C473.5,-540 342.5,-540 342.5,-540 336.5,-540 330.5,-534 330.5,-528 330.5,-528 330.5,-516 330.5,-516 330.5,-510 336.5,-504 342.5,-504 342.5,-504 473.5,-504 473.5,-504 479.5,-504 485.5,-510 485.5,-516 485.5,-516 485.5,-528 485.5,-528 485.5,-534 479.5,-540 473.5,-540"/>
+<text text-anchor="middle" x="408" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
</g>
-<!-- 8->3 -->
-<g id="edge10" class="edge"><title>8->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M642.58,-359.671C630.158,-340.184 607.807,-308.581 582,-288 565.981,-275.225 546.379,-264.542 528.182,-256.192"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="529.38,-252.895 518.82,-252.039 526.542,-259.293 529.38,-252.895"/>
+<!-- 8->1 -->
+<g id="edge3" class="edge">
+<title>8->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M409.2432,-503.8247C411.0006,-476.5213 414,-423.2893 414,-378 414,-378 414,-378 414,-234 414,-187.5145 446.8683,-142.51 471.2376,-115.5311"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="473.9167,-117.7898 478.166,-108.0844 468.7918,-113.0215 473.9167,-117.7898"/>
</g>
<!-- 9 -->
-<g id="node10" class="node"><title>9</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M528,-612C528,-612 416,-612 416,-612 410,-612 404,-606 404,-600 404,-600 404,-588 404,-588 404,-582 410,-576 416,-576 416,-576 528,-576 528,-576 534,-576 540,-582 540,-588 540,-588 540,-600 540,-600 540,-606 534,-612 528,-612"/>
-<text text-anchor="middle" x="472" y="-591.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<g id="node10" class="node">
+<title>9</title>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M883.5,-468C883.5,-468 852.5,-468 852.5,-468 846.5,-468 840.5,-462 840.5,-456 840.5,-456 840.5,-444 840.5,-444 840.5,-438 846.5,-432 852.5,-432 852.5,-432 883.5,-432 883.5,-432 889.5,-432 895.5,-438 895.5,-444 895.5,-444 895.5,-456 895.5,-456 895.5,-462 889.5,-468 883.5,-468"/>
+<text text-anchor="middle" x="868" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
</g>
-<!-- 9->3 -->
-<g id="edge6" class="edge"><title>9->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M472,-575.951C472,-549.292 472,-496.115 472,-451 472,-451 472,-451 472,-377 472,-336.996 472,-290.653 472,-262.08"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="475.5,-262.049 472,-252.049 468.5,-262.049 475.5,-262.049"/>
+<!-- 9->1 -->
+<g id="edge11" class="edge">
+<title>9->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M840.4301,-441.935C818.01,-433.9288 787.3457,-419.4135 770,-396 745.664,-363.1508 751,-346.8816 751,-306 751,-306 751,-306 751,-234 751,-193.1184 760.6491,-173.164 732,-144 706.5561,-118.0989 607.6963,-102.5054 546.5956,-95.1428"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="546.7314,-91.6349 536.392,-93.9473 545.9167,-98.5873 546.7314,-91.6349"/>
</g>
-<!-- 10 -->
-<g id="node11" class="node"><title>10</title>
-<path fill="none" stroke="#d88556" stroke-width="2" d="M373.5,-612C373.5,-612 242.5,-612 242.5,-612 236.5,-612 230.5,-606 230.5,-600 230.5,-600 230.5,-588 230.5,-588 230.5,-582 236.5,-576 242.5,-576 242.5,-576 373.5,-576 373.5,-576 379.5,-576 385.5,-582 385.5,-588 385.5,-588 385.5,-600 385.5,-600 385.5,-606 379.5,-612 373.5,-612"/>
-<text text-anchor="middle" x="308" y="-591.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<!-- 25 -->
+<g id="node26" class="node">
+<title>25</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M1019,-396C1019,-396 913,-396 913,-396 907,-396 901,-390 901,-384 901,-384 901,-372 901,-372 901,-366 907,-360 913,-360 913,-360 1019,-360 1019,-360 1025,-360 1031,-366 1031,-372 1031,-372 1031,-384 1031,-384 1031,-390 1025,-396 1019,-396"/>
+<text text-anchor="middle" x="966" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
</g>
-<!-- 10->3 -->
-<g id="edge5" class="edge"><title>10->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M321.361,-575.721C339.854,-550.027 371,-499.546 371,-451 371,-451 371,-451 371,-377 371,-328.193 411.113,-284.506 440.78,-258.87"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="443.41,-261.233 448.829,-252.129 438.915,-255.867 443.41,-261.233"/>
+<!-- 9->25 -->
+<g id="edge44" class="edge">
+<title>9->25</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M892.7295,-431.8314C904.9162,-422.8779 919.7823,-411.9558 932.9312,-402.2955"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="935.2918,-404.9042 941.2784,-396.1628 931.1473,-399.263 935.2918,-404.9042"/>
</g>
-<!-- 11 -->
-<g id="node12" class="node"><title>11</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M942.5,-612C942.5,-612 911.5,-612 911.5,-612 905.5,-612 899.5,-606 899.5,-600 899.5,-600 899.5,-588 899.5,-588 899.5,-582 905.5,-576 911.5,-576 911.5,-576 942.5,-576 942.5,-576 948.5,-576 954.5,-582 954.5,-588 954.5,-588 954.5,-600 954.5,-600 954.5,-606 948.5,-612 942.5,-612"/>
-<text text-anchor="middle" x="927" y="-591.5" font-family="sans" font-size="10.00">star_rpm</text>
+<!-- 10 -->
+<g id="node11" class="node">
+<title>10</title>
+<path fill="none" stroke="#d89556" stroke-width="2" d="M575.5,-180C575.5,-180 498.5,-180 498.5,-180 492.5,-180 486.5,-174 486.5,-168 486.5,-168 486.5,-156 486.5,-156 486.5,-150 492.5,-144 498.5,-144 498.5,-144 575.5,-144 575.5,-144 581.5,-144 587.5,-150 587.5,-156 587.5,-156 587.5,-168 587.5,-168 587.5,-174 581.5,-180 575.5,-180"/>
+<text text-anchor="middle" x="537" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">alfa_concat_results</text>
</g>
-<!-- 11->3 -->
-<g id="edge8" class="edge"><title>11->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M899.442,-579.32C860.486,-557.807 794,-512.137 794,-451 794,-451 794,-451 794,-377 794,-267.649 636.61,-241.792 541.903,-236.132"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="541.984,-232.631 531.811,-235.59 541.609,-239.621 541.984,-232.631"/>
+<!-- 10->1 -->
+<g id="edge10" class="edge">
+<title>10->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M526.9063,-143.8314C522.4403,-135.7925 517.0925,-126.1666 512.1621,-117.2918"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="515.1456,-115.4551 507.2296,-108.4133 509.0265,-118.8546 515.1456,-115.4551"/>
</g>
-<!-- 33 -->
-<g id="node34" class="node"><title>33</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M980,-540C980,-540 874,-540 874,-540 868,-540 862,-534 862,-528 862,-528 862,-516 862,-516 862,-510 868,-504 874,-504 874,-504 980,-504 980,-504 986,-504 992,-510 992,-516 992,-516 992,-528 992,-528 992,-534 986,-540 980,-540"/>
-<text text-anchor="middle" x="927" y="-519.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
+<!-- 11 -->
+<g id="node12" class="node">
+<title>11</title>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M710.5,-180C710.5,-180 617.5,-180 617.5,-180 611.5,-180 605.5,-174 605.5,-168 605.5,-168 605.5,-156 605.5,-156 605.5,-150 611.5,-144 617.5,-144 617.5,-144 710.5,-144 710.5,-144 716.5,-144 722.5,-150 722.5,-156 722.5,-156 722.5,-168 722.5,-168 722.5,-174 716.5,-180 710.5,-180"/>
+<text text-anchor="middle" x="664" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">prepare_multiqc_config</text>
</g>
-<!-- 11->33 -->
-<g id="edge50" class="edge"><title>11->33</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M927,-575.697C927,-567.983 927,-558.712 927,-550.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="930.5,-550.104 927,-540.104 923.5,-550.104 930.5,-550.104"/>
+<!-- 11->1 -->
+<g id="edge7" class="edge">
+<title>11->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M621.8588,-143.8314C598.6566,-133.828 569.7544,-121.3672 545.6022,-110.9542"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="546.8282,-107.6714 536.2596,-106.9263 544.0568,-114.0995 546.8282,-107.6714"/>
</g>
<!-- 12 -->
-<g id="node13" class="node"><title>12</title>
-<path fill="none" stroke="#5673d8" stroke-width="2" d="M925.5,-324C925.5,-324 848.5,-324 848.5,-324 842.5,-324 836.5,-318 836.5,-312 836.5,-312 836.5,-300 836.5,-300 836.5,-294 842.5,-288 848.5,-288 848.5,-288 925.5,-288 925.5,-288 931.5,-288 937.5,-294 937.5,-300 937.5,-300 937.5,-312 937.5,-312 937.5,-318 931.5,-324 925.5,-324"/>
-<text text-anchor="middle" x="887" y="-303.5" font-family="sans" font-size="10.00">alfa_concat_results</text>
+<g id="node13" class="node">
+<title>12</title>
+<path fill="none" stroke="#78d856" stroke-width="2" d="M1007.5,-324C1007.5,-324 948.5,-324 948.5,-324 942.5,-324 936.5,-318 936.5,-312 936.5,-312 936.5,-300 936.5,-300 936.5,-294 942.5,-288 948.5,-288 948.5,-288 1007.5,-288 1007.5,-288 1013.5,-288 1019.5,-294 1019.5,-300 1019.5,-300 1019.5,-312 1019.5,-312 1019.5,-318 1013.5,-324 1007.5,-324"/>
+<text text-anchor="middle" x="978" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
</g>
-<!-- 12->3 -->
-<g id="edge11" class="edge"><title>12->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M836.088,-293.61C826.763,-291.647 817.103,-289.696 808,-288 716.334,-270.921 609.924,-254.748 541.829,-244.86"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="542.05,-241.356 531.652,-243.388 541.047,-248.284 542.05,-241.356"/>
+<!-- 12->2 -->
+<g id="edge13" class="edge">
+<title>12->2</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M990.3648,-287.8314C995.9509,-279.6232 1002.663,-269.7606 1008.8072,-260.7323"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1011.736,-262.6496 1014.4687,-252.4133 1005.949,-258.7112 1011.736,-262.6496"/>
</g>
<!-- 13 -->
-<g id="node14" class="node"><title>13</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M744,-828C744,-828 632,-828 632,-828 626,-828 620,-822 620,-816 620,-816 620,-804 620,-804 620,-798 626,-792 632,-792 632,-792 744,-792 744,-792 750,-792 756,-798 756,-804 756,-804 756,-816 756,-816 756,-822 750,-828 744,-828"/>
-<text text-anchor="middle" x="688" y="-807.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+<g id="node14" class="node">
+<title>13</title>
+<path fill="none" stroke="#56d8c1" stroke-width="2" d="M983,-684C983,-684 913,-684 913,-684 907,-684 901,-678 901,-672 901,-672 901,-660 901,-660 901,-654 907,-648 913,-648 913,-648 983,-648 983,-648 989,-648 995,-654 995,-660 995,-660 995,-672 995,-672 995,-678 989,-684 983,-684"/>
+<text text-anchor="middle" x="948" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
</g>
-<!-- 13->6 -->
-<g id="edge13" class="edge"><title>13->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M679.101,-791.697C675.003,-783.728 670.051,-774.1 665.507,-765.264"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="668.483,-763.396 660.797,-756.104 662.258,-766.598 668.483,-763.396"/>
+<!-- 13->2 -->
+<g id="edge12" class="edge">
+<title>13->2</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M975.1537,-647.8367C1008.015,-623.4409 1059,-576.7657 1059,-522 1059,-522 1059,-522 1059,-378 1059,-336.9442 1046.4511,-290.8385 1037.0701,-262.1076"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1040.2932,-260.7116 1033.7864,-252.3503 1033.6589,-262.9443 1040.2932,-260.7116"/>
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-<!-- 17 -->
-<g id="node18" class="node"><title>17</title>
-<path fill="none" stroke="#56d85b" stroke-width="2" d="M513.5,-684C513.5,-684 410.5,-684 410.5,-684 404.5,-684 398.5,-678 398.5,-672 398.5,-672 398.5,-660 398.5,-660 398.5,-654 404.5,-648 410.5,-648 410.5,-648 513.5,-648 513.5,-648 519.5,-648 525.5,-654 525.5,-660 525.5,-660 525.5,-672 525.5,-672 525.5,-678 519.5,-684 513.5,-684"/>
-<text text-anchor="middle" x="462" y="-663.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
+<!-- 21 -->
+<g id="node22" class="node">
+<title>21</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M916.5,-612C916.5,-612 827.5,-612 827.5,-612 821.5,-612 815.5,-606 815.5,-600 815.5,-600 815.5,-588 815.5,-588 815.5,-582 821.5,-576 827.5,-576 827.5,-576 916.5,-576 916.5,-576 922.5,-576 928.5,-582 928.5,-588 928.5,-588 928.5,-600 928.5,-600 928.5,-606 922.5,-612 916.5,-612"/>
+<text text-anchor="middle" x="872" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
</g>
-<!-- 13->17 -->
-<g id="edge30" class="edge"><title>13->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M635.545,-791.953C611.565,-783.007 583.362,-770.808 560,-756 544.498,-746.174 510.194,-713.967 486.583,-691.13"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="488.941,-688.542 479.33,-684.085 484.064,-693.563 488.941,-688.542"/>
+<!-- 13->21 -->
+<g id="edge37" class="edge">
+<title>13->21</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M928.822,-647.8314C919.6412,-639.1337 908.4994,-628.5783 898.5224,-619.1265"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="900.8385,-616.4995 891.1719,-612.1628 896.0243,-621.5811 900.8385,-616.4995"/>
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-<!-- 19 -->
-<g id="node20" class="node"><title>19</title>
-<path fill="none" stroke="#78d856" stroke-width="2" d="M1039.5,-756C1039.5,-756 950.5,-756 950.5,-756 944.5,-756 938.5,-750 938.5,-744 938.5,-744 938.5,-732 938.5,-732 938.5,-726 944.5,-720 950.5,-720 950.5,-720 1039.5,-720 1039.5,-720 1045.5,-720 1051.5,-726 1051.5,-732 1051.5,-732 1051.5,-744 1051.5,-744 1051.5,-750 1045.5,-756 1039.5,-756"/>
-<text text-anchor="middle" x="995" y="-735.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+<!-- 23 -->
+<g id="node24" class="node">
+<title>23</title>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M785.5,-612C785.5,-612 712.5,-612 712.5,-612 706.5,-612 700.5,-606 700.5,-600 700.5,-600 700.5,-588 700.5,-588 700.5,-582 706.5,-576 712.5,-576 712.5,-576 785.5,-576 785.5,-576 791.5,-576 797.5,-582 797.5,-588 797.5,-588 797.5,-600 797.5,-600 797.5,-606 791.5,-612 785.5,-612"/>
+<text text-anchor="middle" x="749" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+</g>
+<!-- 13->23 -->
+<g id="edge41" class="edge">
+<title>13->23</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M900.8398,-648.937C872.734,-638.7681 836.8393,-625.781 807.0069,-614.9874"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="808.1459,-611.6775 797.5516,-611.5664 805.7642,-618.2599 808.1459,-611.6775"/>
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-<!-- 13->19 -->
-<g id="edge34" class="edge"><title>13->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M756.189,-794.681C802.17,-784.869 864.435,-771.279 928.304,-756.126"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="929.234,-759.502 938.15,-753.78 927.611,-752.693 929.234,-759.502"/>
+<!-- 33 -->
+<g id="node34" class="node">
+<title>33</title>
+<path fill="none" stroke="#68d856" stroke-width="2" d="M871,-396C871,-396 791,-396 791,-396 785,-396 779,-390 779,-384 779,-384 779,-372 779,-372 779,-366 785,-360 791,-360 791,-360 871,-360 871,-360 877,-360 883,-366 883,-372 883,-372 883,-384 883,-384 883,-390 877,-396 871,-396"/>
+<text text-anchor="middle" x="831" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">generate_alfa_index</text>
+</g>
+<!-- 13->33 -->
+<g id="edge54" class="edge">
+<title>13->33</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M958.5219,-647.7835C974.8242,-617.0198 1002.2081,-553.3062 981,-504 960.9306,-457.3413 913.2283,-422.2406 876.9639,-401.0917"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="878.4396,-397.905 868.0144,-396.0169 874.9868,-403.9942 878.4396,-397.905"/>
</g>
<!-- 14 -->
-<g id="node15" class="node"><title>14</title>
-<path fill="none" stroke="#d87556" stroke-width="2" d="M448,-828C448,-828 364,-828 364,-828 358,-828 352,-822 352,-816 352,-816 352,-804 352,-804 352,-798 358,-792 364,-792 364,-792 448,-792 448,-792 454,-792 460,-798 460,-804 460,-804 460,-816 460,-816 460,-822 454,-828 448,-828"/>
-<text text-anchor="middle" x="406" y="-807.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+<g id="node15" class="node">
+<title>14</title>
+<path fill="none" stroke="#56d8d0" stroke-width="2" d="M685,-828C685,-828 655,-828 655,-828 649,-828 643,-822 643,-816 643,-816 643,-804 643,-804 643,-798 649,-792 655,-792 655,-792 685,-792 685,-792 691,-792 697,-798 697,-804 697,-804 697,-816 697,-816 697,-822 691,-828 685,-828"/>
+<text text-anchor="middle" x="670" y="-807.5" font-family="sans" font-size="10.00" fill="#000000">start</text>
</g>
-<!-- 14->6 -->
-<g id="edge14" class="edge"><title>14->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M460.29,-793.552C496.291,-783.307 543.855,-769.773 582.599,-758.748"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="583.586,-762.106 592.247,-756.003 581.671,-755.374 583.586,-762.106"/>
+<!-- 14->3 -->
+<g id="edge14" class="edge">
+<title>14->3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M697.2112,-807.0018C792.4433,-795.7656 1105,-752.3131 1105,-666 1105,-666 1105,-666 1105,-594 1105,-553.7977 1108.5375,-507.4047 1111.1768,-478.385"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1114.6864,-478.4457 1112.1352,-468.1626 1107.717,-477.7923 1114.6864,-478.4457"/>
</g>
-<!-- 14->7 -->
-<g id="edge16" class="edge"><title>14->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M404.517,-791.697C403.856,-783.983 403.061,-774.712 402.324,-766.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="405.807,-765.769 401.466,-756.104 398.833,-766.367 405.807,-765.769"/>
+<!-- 26 -->
+<g id="node27" class="node">
+<title>26</title>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M733,-756C733,-756 607,-756 607,-756 601,-756 595,-750 595,-744 595,-744 595,-732 595,-732 595,-726 601,-720 607,-720 607,-720 733,-720 733,-720 739,-720 745,-726 745,-732 745,-732 745,-744 745,-744 745,-750 739,-756 733,-756"/>
+<text text-anchor="middle" x="670" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
</g>
-<!-- 15 -->
-<g id="node16" class="node"><title>15</title>
-<path fill="none" stroke="#56d0d8" stroke-width="2" d="M586,-828C586,-828 490,-828 490,-828 484,-828 478,-822 478,-816 478,-816 478,-804 478,-804 478,-798 484,-792 490,-792 490,-792 586,-792 586,-792 592,-792 598,-798 598,-804 598,-804 598,-816 598,-816 598,-822 592,-828 586,-828"/>
-<text text-anchor="middle" x="538" y="-807.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
+<!-- 14->26 -->
+<g id="edge45" class="edge">
+<title>14->26</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M670,-791.8314C670,-784.131 670,-774.9743 670,-766.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="673.5001,-766.4132 670,-756.4133 666.5001,-766.4133 673.5001,-766.4132"/>
</g>
-<!-- 15->7 -->
-<g id="edge15" class="edge"><title>15->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M504.241,-791.876C485.78,-782.512 462.718,-770.814 442.983,-760.803"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="444.39,-757.592 433.888,-756.19 441.223,-763.835 444.39,-757.592"/>
+<!-- 28 -->
+<g id="node29" class="node">
+<title>28</title>
+<path fill="none" stroke="#59d856" stroke-width="2" d="M536,-756C536,-756 426,-756 426,-756 420,-756 414,-750 414,-744 414,-744 414,-732 414,-732 414,-726 420,-720 426,-720 426,-720 536,-720 536,-720 542,-720 548,-726 548,-732 548,-732 548,-744 548,-744 548,-750 542,-756 536,-756"/>
+<text text-anchor="middle" x="481" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
</g>
-<!-- 18 -->
-<g id="node19" class="node"><title>18</title>
-<path fill="none" stroke="#56d8d8" stroke-width="2" d="M355.5,-684C355.5,-684 268.5,-684 268.5,-684 262.5,-684 256.5,-678 256.5,-672 256.5,-672 256.5,-660 256.5,-660 256.5,-654 262.5,-648 268.5,-648 268.5,-648 355.5,-648 355.5,-648 361.5,-648 367.5,-654 367.5,-660 367.5,-660 367.5,-672 367.5,-672 367.5,-678 361.5,-684 355.5,-684"/>
-<text text-anchor="middle" x="312" y="-663.5" font-family="sans" font-size="10.00">quantification_salmon</text>
+<!-- 14->28 -->
+<g id="edge46" class="edge">
+<title>14->28</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M642.9209,-799.6842C615.6776,-789.3058 572.8354,-772.9849 538.0613,-759.7376"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="539.0777,-756.3795 528.4868,-756.0902 536.5857,-762.9209 539.0777,-756.3795"/>
</g>
-<!-- 15->18 -->
-<g id="edge32" class="edge"><title>15->18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M531.875,-791.656C523.906,-771.551 508.088,-738.779 484,-720 467.061,-706.794 418.711,-692.487 377.572,-682.07"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="378.387,-678.666 367.837,-679.642 376.693,-685.458 378.387,-678.666"/>
+<!-- 15 -->
+<g id="node16" class="node">
+<title>15</title>
+<path fill="none" stroke="#d87556" stroke-width="2" d="M726,-684C726,-684 614,-684 614,-684 608,-684 602,-678 602,-672 602,-672 602,-660 602,-660 602,-654 608,-648 614,-648 614,-648 726,-648 726,-648 732,-648 738,-654 738,-660 738,-660 738,-672 738,-672 738,-678 732,-684 726,-684"/>
+<text text-anchor="middle" x="670" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
</g>
-<!-- 21 -->
-<g id="node22" class="node"><title>21</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M908.5,-756C908.5,-756 835.5,-756 835.5,-756 829.5,-756 823.5,-750 823.5,-744 823.5,-744 823.5,-732 823.5,-732 823.5,-726 829.5,-720 835.5,-720 835.5,-720 908.5,-720 908.5,-720 914.5,-720 920.5,-726 920.5,-732 920.5,-732 920.5,-744 920.5,-744 920.5,-750 914.5,-756 908.5,-756"/>
-<text text-anchor="middle" x="872" y="-735.5" font-family="sans" font-size="10.00">map_genome_star</text>
+<!-- 15->4 -->
+<g id="edge15" class="edge">
+<title>15->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M601.5835,-649.8725C598.3486,-649.2167 595.1418,-648.5886 592,-648 485.2072,-627.9937 454.9352,-630.5714 344.1102,-612.1387"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="344.6531,-608.681 334.2108,-610.4724 343.4911,-615.5839 344.6531,-608.681"/>
+</g>
+<!-- 19 -->
+<g id="node20" class="node">
+<title>19</title>
+<path fill="none" stroke="#5673d8" stroke-width="2" d="M596.5,-612C596.5,-612 493.5,-612 493.5,-612 487.5,-612 481.5,-606 481.5,-600 481.5,-600 481.5,-588 481.5,-588 481.5,-582 487.5,-576 493.5,-576 493.5,-576 596.5,-576 596.5,-576 602.5,-576 608.5,-582 608.5,-588 608.5,-588 608.5,-600 608.5,-600 608.5,-606 602.5,-612 596.5,-612"/>
+<text text-anchor="middle" x="545" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
+</g>
+<!-- 15->19 -->
+<g id="edge33" class="edge">
+<title>15->19</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M638.4572,-647.8314C622.3209,-638.5368 602.5014,-627.1208 585.2728,-617.1971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="586.945,-614.1212 576.5327,-612.1628 583.4511,-620.187 586.945,-614.1212"/>
</g>
<!-- 15->21 -->
-<g id="edge38" class="edge"><title>15->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M598.122,-794.856C602.477,-793.875 606.804,-792.914 611,-792 680.392,-776.878 760.474,-760.822 813.437,-750.397"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="814.191,-753.816 823.329,-748.454 812.842,-746.947 814.191,-753.816"/>
+<g id="edge38" class="edge">
+<title>15->21</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M720.7124,-647.9243C748.327,-638.0815 782.675,-625.8386 811.6601,-615.5073"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="813.0223,-618.7375 821.2667,-612.0831 810.6721,-612.1438 813.0223,-618.7375"/>
</g>
<!-- 16 -->
-<g id="node17" class="node"><title>16</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M714,-540C714,-540 638,-540 638,-540 632,-540 626,-534 626,-528 626,-528 626,-516 626,-516 626,-510 632,-504 638,-504 638,-504 714,-504 714,-504 720,-504 726,-510 726,-516 726,-516 726,-528 726,-528 726,-534 720,-540 714,-540"/>
-<text text-anchor="middle" x="676" y="-519.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
-</g>
-<!-- 16->8 -->
-<g id="edge17" class="edge"><title>16->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M673.226,-503.871C669.306,-479.67 662.105,-435.211 657.437,-406.393"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="660.838,-405.501 655.784,-396.189 653.928,-406.62 660.838,-405.501"/>
-</g>
-<!-- 17->9 -->
-<g id="edge18" class="edge"><title>17->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M464.472,-647.697C465.574,-639.983 466.898,-630.712 468.127,-622.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="471.607,-622.499 469.557,-612.104 464.677,-621.509 471.607,-622.499"/>
-</g>
-<!-- 17->10 -->
-<g id="edge20" class="edge"><title>17->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M424.327,-647.876C403.368,-638.349 377.095,-626.407 354.823,-616.283"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="356.102,-613.02 345.55,-612.068 353.206,-619.393 356.102,-613.02"/>
-</g>
-<!-- 18->9 -->
-<g id="edge19" class="edge"><title>18->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M351.14,-647.876C373.013,-638.307 400.457,-626.3 423.662,-616.148"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="425.228,-619.283 432.987,-612.068 422.422,-612.87 425.228,-619.283"/>
-</g>
-<!-- 18->10 -->
-<g id="edge21" class="edge"><title>18->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M311.011,-647.697C310.57,-639.983 310.041,-630.712 309.549,-622.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="313.042,-621.888 308.977,-612.104 306.054,-622.288 313.042,-621.888"/>
-</g>
-<!-- 19->11 -->
-<g id="edge24" class="edge"><title>19->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M998.427,-719.921C1001.3,-701.221 1003.33,-670.855 992,-648 985.547,-634.983 974.25,-624.061 962.865,-615.579"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="964.832,-612.685 954.627,-609.839 960.83,-618.428 964.832,-612.685"/>
+<g id="node17" class="node">
+<title>16</title>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M293,-684C293,-684 209,-684 209,-684 203,-684 197,-678 197,-672 197,-672 197,-660 197,-660 197,-654 203,-648 209,-648 209,-648 293,-648 293,-648 299,-648 305,-654 305,-660 305,-660 305,-672 305,-672 305,-678 299,-684 293,-684"/>
+<text text-anchor="middle" x="251" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
+</g>
+<!-- 16->4 -->
+<g id="edge16" class="edge">
+<title>16->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M251,-647.8314C251,-640.131 251,-630.9743 251,-622.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="254.5001,-622.4132 251,-612.4133 247.5001,-622.4133 254.5001,-622.4132"/>
+</g>
+<!-- 16->5 -->
+<g id="edge18" class="edge">
+<title>16->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M206.5878,-647.8314C182.8396,-638.1162 153.4254,-626.0831 128.4336,-615.8592"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="129.6736,-612.585 119.0929,-612.038 127.0231,-619.0638 129.6736,-612.585"/>
</g>
-<!-- 20 -->
-<g id="node21" class="node"><title>20</title>
-<path fill="none" stroke="#56d8b9" stroke-width="2" d="M955,-684C955,-684 805,-684 805,-684 799,-684 793,-678 793,-672 793,-672 793,-660 793,-660 793,-654 799,-648 805,-648 805,-648 955,-648 955,-648 961,-648 967,-654 967,-660 967,-660 967,-672 967,-672 967,-678 961,-684 955,-684"/>
-<text text-anchor="middle" x="880" y="-663.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<!-- 17 -->
+<g id="node18" class="node">
+<title>17</title>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M444,-684C444,-684 348,-684 348,-684 342,-684 336,-678 336,-672 336,-672 336,-660 336,-660 336,-654 342,-648 348,-648 348,-648 444,-648 444,-648 450,-648 456,-654 456,-660 456,-660 456,-672 456,-672 456,-678 450,-684 444,-684"/>
+<text text-anchor="middle" x="396" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
</g>
-<!-- 19->20 -->
-<g id="edge37" class="edge"><title>19->20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M966.868,-719.876C951.832,-710.724 933.133,-699.342 916.94,-689.485"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="918.602,-686.4 908.24,-684.19 914.962,-692.379 918.602,-686.4"/>
+<!-- 17->5 -->
+<g id="edge17" class="edge">
+<title>17->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M335.9989,-652.5418C286.4409,-641.426 215.4925,-625.5123 160.0734,-613.0819"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="160.7906,-609.6559 150.267,-610.8823 159.2585,-616.4861 160.7906,-609.6559"/>
</g>
-<!-- 26 -->
-<g id="node27" class="node"><title>26</title>
-<path fill="none" stroke="#56d86b" stroke-width="2" d="M746,-612C746,-612 658,-612 658,-612 652,-612 646,-606 646,-600 646,-600 646,-588 646,-588 646,-582 652,-576 658,-576 658,-576 746,-576 746,-576 752,-576 758,-582 758,-588 758,-588 758,-600 758,-600 758,-606 752,-612 746,-612"/>
-<text text-anchor="middle" x="702" y="-591.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
-</g>
-<!-- 19->26 -->
-<g id="edge44" class="edge"><title>19->26</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M996.5,-719.984C997.261,-699.884 995.174,-666.809 976,-648 947.195,-619.744 839.886,-605.821 768.42,-599.541"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="768.409,-596.027 758.149,-598.669 767.817,-603.002 768.409,-596.027"/>
-</g>
-<!-- 20->11 -->
-<g id="edge23" class="edge"><title>20->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M891.618,-647.697C897.139,-639.474 903.847,-629.483 909.932,-620.421"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="912.847,-622.358 915.516,-612.104 907.035,-618.456 912.847,-622.358"/>
-</g>
-<!-- 20->26 -->
-<g id="edge43" class="edge"><title>20->26</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M836.456,-647.876C811.798,-638.179 780.777,-625.98 754.746,-615.743"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="755.989,-612.471 745.402,-612.068 753.428,-618.985 755.989,-612.471"/>
-</g>
-<!-- 21->11 -->
-<g id="edge22" class="edge"><title>21->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M916.362,-719.889C941.372,-709.243 968.986,-695.447 976,-684 984.359,-670.357 981.832,-662.899 976,-648 971.803,-637.279 964.308,-627.427 956.422,-619.201"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="958.76,-616.592 949.153,-612.125 953.877,-621.608 958.76,-616.592"/>
-</g>
-<!-- 21->20 -->
-<g id="edge36" class="edge"><title>21->20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M873.978,-719.697C874.859,-711.983 875.919,-702.712 876.901,-694.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="880.387,-694.437 878.045,-684.104 873.432,-693.642 880.387,-694.437"/>
-</g>
-<!-- 21->26 -->
-<g id="edge41" class="edge"><title>21->26</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M823.356,-730.106C753.776,-719.753 632.766,-699.73 620,-684 609.918,-671.576 612.35,-662.053 620,-648 626.913,-635.301 638.322,-625.181 650.465,-617.33"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="652.587,-620.14 659.382,-612.011 649.001,-614.128 652.587,-620.14"/>
+<!-- 20 -->
+<g id="node21" class="node">
+<title>20</title>
+<path fill="none" stroke="#9fd856" stroke-width="2" d="M451.5,-612C451.5,-612 364.5,-612 364.5,-612 358.5,-612 352.5,-606 352.5,-600 352.5,-600 352.5,-588 352.5,-588 352.5,-582 358.5,-576 364.5,-576 364.5,-576 451.5,-576 451.5,-576 457.5,-576 463.5,-582 463.5,-588 463.5,-588 463.5,-600 463.5,-600 463.5,-606 457.5,-612 451.5,-612"/>
+<text text-anchor="middle" x="408" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
+</g>
+<!-- 17->20 -->
+<g id="edge35" class="edge">
+<title>17->20</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M399.0281,-647.8314C400.3115,-640.131 401.8376,-630.9743 403.2639,-622.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="406.7394,-622.8526 404.9311,-612.4133 399.8347,-621.7018 406.7394,-622.8526"/>
+</g>
+<!-- 17->23 -->
+<g id="edge42" class="edge">
+<title>17->23</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M456.1526,-650.0535C459.1398,-649.3415 462.1014,-648.6529 465,-648 542.4822,-630.5481 632.6938,-614.0378 690.2899,-603.9737"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="691.0497,-607.3942 700.3017,-602.2319 689.8498,-600.4978 691.0497,-607.3942"/>
+</g>
+<!-- 18 -->
+<g id="node19" class="node">
+<title>18</title>
+<path fill="none" stroke="#97d856" stroke-width="2" d="M652,-396C652,-396 576,-396 576,-396 570,-396 564,-390 564,-384 564,-384 564,-372 564,-372 564,-366 570,-360 576,-360 576,-360 652,-360 652,-360 658,-360 664,-366 664,-372 664,-372 664,-384 664,-384 664,-390 658,-396 652,-396"/>
+<text text-anchor="middle" x="614" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">merge_TIN_scores</text>
+</g>
+<!-- 18->6 -->
+<g id="edge19" class="edge">
+<title>18->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M600.7017,-359.7623C582.3979,-334.66 549.3242,-289.3017 528.2989,-260.4671"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="530.9101,-258.1076 522.1903,-252.0896 525.2541,-262.2318 530.9101,-258.1076"/>
+</g>
+<!-- 19->7 -->
+<g id="edge20" class="edge">
+<title>19->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M481.3072,-578.2584C478.1608,-577.4922 475.0451,-576.736 472,-576 422.0988,-563.9387 365.9864,-550.6455 321.9148,-540.2664"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="322.6658,-536.8476 312.1299,-537.9633 321.062,-543.6614 322.6658,-536.8476"/>
+</g>
+<!-- 19->8 -->
+<g id="edge22" class="edge">
+<title>19->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M510.4291,-575.8314C492.5815,-566.4516 470.6226,-554.9112 451.62,-544.9244"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="453.0401,-541.7168 442.5598,-540.1628 449.7836,-547.9132 453.0401,-541.7168"/>
+</g>
+<!-- 20->7 -->
+<g id="edge21" class="edge">
+<title>20->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M366.6159,-575.8314C344.6818,-566.2018 317.5608,-554.295 294.4069,-544.1299"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="295.65,-540.8532 285.0865,-540.038 292.836,-547.2627 295.65,-540.8532"/>
+</g>
+<!-- 20->8 -->
+<g id="edge23" class="edge">
+<title>20->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M408,-575.8314C408,-568.131 408,-558.9743 408,-550.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="411.5001,-550.4132 408,-540.4133 404.5001,-550.4133 411.5001,-550.4132"/>
+</g>
+<!-- 21->9 -->
+<g id="edge25" class="edge">
+<title>21->9</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M923.0855,-575.9348C939.0666,-567.5922 954.8895,-555.9115 964,-540 971.9502,-526.115 972.0775,-517.8114 964,-504 951.3587,-482.3853 926.5324,-468.7542 905.2939,-460.5947"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="906.4394,-457.2873 895.8448,-457.2217 904.086,-463.8799 906.4394,-457.2873"/>
</g>
<!-- 22 -->
-<g id="node23" class="node"><title>22</title>
-<path fill="none" stroke="#5682d8" stroke-width="2" d="M941.5,-396C941.5,-396 860.5,-396 860.5,-396 854.5,-396 848.5,-390 848.5,-384 848.5,-384 848.5,-372 848.5,-372 848.5,-366 854.5,-360 860.5,-360 860.5,-360 941.5,-360 941.5,-360 947.5,-360 953.5,-366 953.5,-372 953.5,-372 953.5,-384 953.5,-384 953.5,-390 947.5,-396 941.5,-396"/>
-<text text-anchor="middle" x="901" y="-375.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
+<g id="node23" class="node">
+<title>22</title>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M943,-540C943,-540 793,-540 793,-540 787,-540 781,-534 781,-528 781,-528 781,-516 781,-516 781,-510 787,-504 793,-504 793,-504 943,-504 943,-504 949,-504 955,-510 955,-516 955,-516 955,-528 955,-528 955,-534 949,-540 943,-540"/>
+<text text-anchor="middle" x="868" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
</g>
-<!-- 22->12 -->
-<g id="edge25" class="edge"><title>22->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M897.539,-359.697C895.997,-351.983 894.142,-342.712 892.422,-334.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="895.814,-333.224 890.421,-324.104 888.95,-334.597 895.814,-333.224"/>
+<!-- 21->22 -->
+<g id="edge39" class="edge">
+<title>21->22</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M870.9906,-575.8314C870.5628,-568.131 870.0541,-558.9743 869.5787,-550.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="873.0724,-550.2037 869.023,-540.4133 866.0831,-550.592 873.0724,-550.2037"/>
</g>
-<!-- 23 -->
-<g id="node24" class="node"><title>23</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M758,-900C758,-900 632,-900 632,-900 626,-900 620,-894 620,-888 620,-888 620,-876 620,-876 620,-870 626,-864 632,-864 632,-864 758,-864 758,-864 764,-864 770,-870 770,-876 770,-876 770,-888 770,-888 770,-894 764,-900 758,-900"/>
-<text text-anchor="middle" x="695" y="-879.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
-</g>
-<!-- 23->13 -->
-<g id="edge26" class="edge"><title>23->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M693.27,-863.697C692.498,-855.983 691.571,-846.712 690.711,-838.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="694.188,-837.706 689.71,-828.104 687.223,-838.403 694.188,-837.706"/>
+<!-- 29 -->
+<g id="node30" class="node">
+<title>29</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M721,-468C721,-468 633,-468 633,-468 627,-468 621,-462 621,-456 621,-456 621,-444 621,-444 621,-438 627,-432 633,-432 633,-432 721,-432 721,-432 727,-432 733,-438 733,-444 733,-444 733,-456 733,-456 733,-462 727,-468 721,-468"/>
+<text text-anchor="middle" x="677" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
+</g>
+<!-- 21->29 -->
+<g id="edge48" class="edge">
+<title>21->29</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M833.0741,-575.9889C813.9619,-566.4078 791.0168,-553.7712 772,-540 745.4766,-520.7929 718.7038,-494.6827 700.3711,-475.5321"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="702.7101,-472.9114 693.2969,-468.0491 697.6233,-477.7203 702.7101,-472.9114"/>
+</g>
+<!-- 22->9 -->
+<g id="edge24" class="edge">
+<title>22->9</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M868,-503.8314C868,-496.131 868,-486.9743 868,-478.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="871.5001,-478.4132 868,-468.4133 864.5001,-478.4133 871.5001,-478.4132"/>
+</g>
+<!-- 22->29 -->
+<g id="edge47" class="edge">
+<title>22->29</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M819.8026,-503.8314C793.8034,-494.0306 761.5464,-481.8709 734.2719,-471.5894"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="735.4426,-468.2904 724.8508,-468.038 732.9734,-474.8404 735.4426,-468.2904"/>
+</g>
+<!-- 23->9 -->
+<g id="edge26" class="edge">
+<title>23->9</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M749.5135,-575.9721C750.9318,-556.3987 755.8051,-525.1141 772,-504 786.8694,-484.614 810.8089,-471.1278 831.0611,-462.4813"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="832.39,-465.7194 840.3551,-458.7332 829.7718,-459.2274 832.39,-465.7194"/>
+</g>
+<!-- 23->22 -->
+<g id="edge40" class="edge">
+<title>23->22</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M779.0287,-575.8314C794.2496,-566.6221 812.9128,-555.3301 829.2083,-545.4706"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="831.2369,-548.3341 837.9809,-540.1628 827.6132,-542.345 831.2369,-548.3341"/>
+</g>
+<!-- 23->29 -->
+<g id="edge49" class="edge">
+<title>23->29</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M728.7914,-575.6949C719.1245,-565.9488 708.1319,-553.2551 701,-540 690.6238,-520.7152 684.5095,-496.6485 681.0516,-478.2556"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="684.4593,-477.4204 679.3105,-468.1608 677.5612,-478.6102 684.4593,-477.4204"/>
</g>
<!-- 24 -->
-<g id="node25" class="node"><title>24</title>
-<path fill="none" stroke="#d89556" stroke-width="2" d="M359.5,-900C359.5,-900 272.5,-900 272.5,-900 266.5,-900 260.5,-894 260.5,-888 260.5,-888 260.5,-876 260.5,-876 260.5,-870 266.5,-864 272.5,-864 272.5,-864 359.5,-864 359.5,-864 365.5,-864 371.5,-870 371.5,-876 371.5,-876 371.5,-888 371.5,-888 371.5,-894 365.5,-900 359.5,-900"/>
-<text text-anchor="middle" x="316" y="-879.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
-</g>
-<!-- 24->14 -->
-<g id="edge27" class="edge"><title>24->14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M338.247,-863.697C349.582,-854.881 363.53,-844.032 375.819,-834.474"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="378.264,-837.007 384.009,-828.104 373.966,-831.481 378.264,-837.007"/>
+<g id="node25" class="node">
+<title>24</title>
+<path fill="none" stroke="#ced856" stroke-width="2" d="M695.5,-252C695.5,-252 614.5,-252 614.5,-252 608.5,-252 602.5,-246 602.5,-240 602.5,-240 602.5,-228 602.5,-228 602.5,-222 608.5,-216 614.5,-216 614.5,-216 695.5,-216 695.5,-216 701.5,-216 707.5,-222 707.5,-228 707.5,-228 707.5,-240 707.5,-240 707.5,-246 701.5,-252 695.5,-252"/>
+<text text-anchor="middle" x="655" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
+</g>
+<!-- 24->10 -->
+<g id="edge27" class="edge">
+<title>24->10</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M625.2236,-215.8314C610.1307,-206.6221 591.6243,-195.3301 575.4657,-185.4706"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="577.1263,-182.3838 566.7669,-180.1628 573.4802,-188.3593 577.1263,-182.3838"/>
+</g>
+<!-- 25->12 -->
+<g id="edge28" class="edge">
+<title>25->12</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M969.0281,-359.8314C970.3115,-352.131 971.8376,-342.9743 973.2639,-334.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="976.7394,-334.8526 974.9311,-324.4133 969.8347,-333.7018 976.7394,-334.8526"/>
</g>
<!-- 31 -->
-<g id="node32" class="node"><title>31</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M321.5,-828C321.5,-828 150.5,-828 150.5,-828 144.5,-828 138.5,-822 138.5,-816 138.5,-816 138.5,-804 138.5,-804 138.5,-798 144.5,-792 150.5,-792 150.5,-792 321.5,-792 321.5,-792 327.5,-792 333.5,-798 333.5,-804 333.5,-804 333.5,-816 333.5,-816 333.5,-822 327.5,-828 321.5,-828"/>
-<text text-anchor="middle" x="236" y="-807.5" font-family="sans" font-size="10.00">concatenate_transcriptome_and_genome</text>
-</g>
-<!-- 24->31 -->
-<g id="edge49" class="edge"><title>24->31</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M296.225,-863.697C286.246,-854.965 273.989,-844.24 263.143,-834.75"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="265.378,-832.055 255.548,-828.104 260.769,-837.323 265.378,-832.055"/>
-</g>
-<!-- 25 -->
-<g id="node26" class="node"><title>25</title>
-<path fill="none" stroke="#c6d856" stroke-width="2" d="M590,-900C590,-900 480,-900 480,-900 474,-900 468,-894 468,-888 468,-888 468,-876 468,-876 468,-870 474,-864 480,-864 480,-864 590,-864 590,-864 596,-864 602,-870 602,-876 602,-876 602,-888 602,-888 602,-894 596,-900 590,-900"/>
-<text text-anchor="middle" x="535" y="-879.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
-</g>
-<!-- 25->15 -->
-<g id="edge28" class="edge"><title>25->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M535.742,-863.697C536.072,-855.983 536.469,-846.712 536.838,-838.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="540.335,-838.245 537.267,-828.104 533.342,-837.945 540.335,-838.245"/>
-</g>
-<!-- 26->16 -->
-<g id="edge29" class="edge"><title>26->16</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M695.573,-575.697C692.645,-567.813 689.113,-558.304 685.86,-549.546"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="689.116,-548.26 682.353,-540.104 682.554,-550.697 689.116,-548.26"/>
+<g id="node32" class="node">
+<title>31</title>
+<path fill="none" stroke="#56d8b1" stroke-width="2" d="M846,-324C846,-324 816,-324 816,-324 810,-324 804,-318 804,-312 804,-312 804,-300 804,-300 804,-294 810,-288 816,-288 816,-288 846,-288 846,-288 852,-288 858,-294 858,-300 858,-300 858,-312 858,-312 858,-318 852,-324 846,-324"/>
+<text text-anchor="middle" x="831" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
+</g>
+<!-- 25->31 -->
+<g id="edge52" class="edge">
+<title>25->31</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M931.9338,-359.8314C912.1547,-349.2825 887.2517,-336.0009 867.1309,-325.2698"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="868.7289,-322.1555 858.2583,-320.5378 865.4348,-328.3319 868.7289,-322.1555"/>
+</g>
+<!-- 26->15 -->
+<g id="edge29" class="edge">
+<title>26->15</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M670,-719.8314C670,-712.131 670,-702.9743 670,-694.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="673.5001,-694.4132 670,-684.4133 666.5001,-694.4133 673.5001,-694.4132"/>
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<!-- 27 -->
-<g id="node28" class="node"><title>27</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M283.5,-756C283.5,-756 198.5,-756 198.5,-756 192.5,-756 186.5,-750 186.5,-744 186.5,-744 186.5,-732 186.5,-732 186.5,-726 192.5,-720 198.5,-720 198.5,-720 283.5,-720 283.5,-720 289.5,-720 295.5,-726 295.5,-732 295.5,-732 295.5,-744 295.5,-744 295.5,-750 289.5,-756 283.5,-756"/>
-<text text-anchor="middle" x="241" y="-735.5" font-family="sans" font-size="10.00">create_index_salmon</text>
+<g id="node28" class="node">
+<title>27</title>
+<path fill="none" stroke="#56d873" stroke-width="2" d="M324.5,-756C324.5,-756 237.5,-756 237.5,-756 231.5,-756 225.5,-750 225.5,-744 225.5,-744 225.5,-732 225.5,-732 225.5,-726 231.5,-720 237.5,-720 237.5,-720 324.5,-720 324.5,-720 330.5,-720 336.5,-726 336.5,-732 336.5,-732 336.5,-744 336.5,-744 336.5,-750 330.5,-756 324.5,-756"/>
+<text text-anchor="middle" x="281" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
</g>
-<!-- 27->17 -->
-<g id="edge31" class="edge"><title>27->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M294.78,-719.966C325.927,-710.1 365.323,-697.622 398.052,-687.255"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="399.502,-690.467 407.979,-684.111 397.389,-683.794 399.502,-690.467"/>
-</g>
-<!-- 27->18 -->
-<g id="edge33" class="edge"><title>27->18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M258.551,-719.697C267.234,-711.135 277.863,-700.656 287.348,-691.304"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="289.988,-693.617 294.651,-684.104 285.073,-688.633 289.988,-693.617"/>
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-<!-- 28 -->
-<g id="node29" class="node"><title>28</title>
-<path fill="none" stroke="#5663d8" stroke-width="2" d="M1030,-828C1030,-828 960,-828 960,-828 954,-828 948,-822 948,-816 948,-816 948,-804 948,-804 948,-798 954,-792 960,-792 960,-792 1030,-792 1030,-792 1036,-792 1042,-798 1042,-804 1042,-804 1042,-816 1042,-816 1042,-822 1036,-828 1030,-828"/>
-<text text-anchor="middle" x="995" y="-807.5" font-family="sans" font-size="10.00">create_index_star</text>
-</g>
-<!-- 28->19 -->
-<g id="edge35" class="edge"><title>28->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M995,-791.697C995,-783.983 995,-774.712 995,-766.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="998.5,-766.104 995,-756.104 991.5,-766.104 998.5,-766.104"/>
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-<!-- 28->21 -->
-<g id="edge39" class="edge"><title>28->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M964.911,-791.876C948.68,-782.639 928.458,-771.131 911.029,-761.212"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="912.627,-758.094 902.205,-756.19 909.165,-764.178 912.627,-758.094"/>
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-<!-- 34 -->
-<g id="node35" class="node"><title>34</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1126,-540C1126,-540 1046,-540 1046,-540 1040,-540 1034,-534 1034,-528 1034,-528 1034,-516 1034,-516 1034,-510 1040,-504 1046,-504 1046,-504 1126,-504 1126,-504 1132,-504 1138,-510 1138,-516 1138,-516 1138,-528 1138,-528 1138,-534 1132,-540 1126,-540"/>
-<text text-anchor="middle" x="1086" y="-519.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
-</g>
-<!-- 28->34 -->
-<g id="edge51" class="edge"><title>28->34</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1025.63,-791.97C1038.75,-783.028 1052.89,-770.827 1061,-756 1097.51,-689.252 1094.02,-595.687 1089.49,-550.104"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1092.96,-549.666 1088.4,-540.104 1086,-550.425 1092.96,-549.666"/>
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-<!-- 29 -->
-<g id="node30" class="node"><title>29</title>
-<path fill="none" stroke="#b6d856" stroke-width="2" d="M942,-468C942,-468 912,-468 912,-468 906,-468 900,-462 900,-456 900,-456 900,-444 900,-444 900,-438 906,-432 912,-432 912,-432 942,-432 942,-432 948,-432 954,-438 954,-444 954,-444 954,-456 954,-456 954,-462 948,-468 942,-468"/>
-<text text-anchor="middle" x="927" y="-447.5" font-family="sans" font-size="10.00">alfa_qc</text>
-</g>
-<!-- 29->22 -->
-<g id="edge40" class="edge"><title>29->22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M920.573,-431.697C917.645,-423.813 914.113,-414.304 910.86,-405.546"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="914.116,-404.26 907.353,-396.104 907.554,-406.697 914.116,-404.26"/>
+<!-- 27->16 -->
+<g id="edge30" class="edge">
+<title>27->16</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M273.4297,-719.8314C270.1507,-711.9617 266.238,-702.5712 262.6055,-693.8533"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="265.7492,-692.2979 258.6722,-684.4133 259.2876,-694.9902 265.7492,-692.2979"/>
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<!-- 30 -->
-<g id="node31" class="node"><title>30</title>
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-<text text-anchor="middle" x="702" y="-663.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
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-<g id="edge42" class="edge"><title>30->26</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="242.557,-766.328 239.778,-756.104 235.575,-765.83 242.557,-766.328"/>
+<g id="node31" class="node">
+<title>30</title>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M571.5,-684C571.5,-684 486.5,-684 486.5,-684 480.5,-684 474.5,-678 474.5,-672 474.5,-672 474.5,-660 474.5,-660 474.5,-654 480.5,-648 486.5,-648 486.5,-648 571.5,-648 571.5,-648 577.5,-648 583.5,-654 583.5,-660 583.5,-660 583.5,-672 583.5,-672 583.5,-678 577.5,-684 571.5,-684"/>
+<text text-anchor="middle" x="529" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
+</g>
+<!-- 27->30 -->
+<g id="edge51" class="edge">
+<title>27->30</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M336.656,-721.8418C374.5721,-710.8339 424.8861,-696.2266 464.5445,-684.7129"/>
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+</g>
+<!-- 28->17 -->
+<g id="edge31" class="edge">
+<title>28->17</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M459.5509,-719.8314C449.1822,-711.0485 436.5771,-700.3712 425.3354,-690.8489"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="427.3349,-687.9556 417.4422,-684.1628 422.8105,-693.297 427.3349,-687.9556"/>
+</g>
+<!-- 29->18 -->
+<g id="edge32" class="edge">
+<title>29->18</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M661.1024,-431.8314C653.7722,-423.454 644.934,-413.3531 636.9031,-404.1749"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="639.3307,-401.6343 630.1116,-396.4133 634.0627,-406.2438 639.3307,-401.6343"/>
+</g>
+<!-- 30->19 -->
+<g id="edge34" class="edge">
+<title>30->19</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M533.0375,-647.8314C534.7487,-640.131 536.7835,-630.9743 538.6852,-622.4166"/>
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+</g>
+<!-- 30->20 -->
+<g id="edge36" class="edge">
+<title>30->20</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M498.4666,-647.8314C482.9899,-638.6221 464.0131,-627.3301 447.4437,-617.4706"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="448.9071,-614.2687 438.5236,-612.1628 445.3276,-620.2843 448.9071,-614.2687"/>
+</g>
+<!-- 31->24 -->
+<g id="edge43" class="edge">
+<title>31->24</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M803.8857,-294.9078C778.6315,-284.5765 740.2554,-268.8772 708.7903,-256.0051"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="709.85,-252.6571 699.2693,-252.1102 707.1996,-259.136 709.85,-252.6571"/>
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<!-- 32 -->
-<g id="node33" class="node"><title>32</title>
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-<text text-anchor="middle" x="60" y="-807.5" font-family="sans" font-size="10.00">extract_decoys_salmon</text>
-</g>
-<!-- 32->27 -->
-<g id="edge46" class="edge"><title>32->27</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="930.5,-478.104 927,-468.104 923.5,-478.104 930.5,-478.104"/>
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-<g id="edge48" class="edge"><title>34->29</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="964.604,-463.731 954.041,-462.905 961.783,-470.138 964.604,-463.731"/>
+<g id="node33" class="node">
+<title>32</title>
+<path fill="none" stroke="#d8c356" stroke-width="2" d="M636.5,-540C636.5,-540 515.5,-540 515.5,-540 509.5,-540 503.5,-534 503.5,-528 503.5,-528 503.5,-516 503.5,-516 503.5,-510 509.5,-504 515.5,-504 515.5,-504 636.5,-504 636.5,-504 642.5,-504 648.5,-510 648.5,-516 648.5,-516 648.5,-528 648.5,-528 648.5,-534 642.5,-540 636.5,-540"/>
+<text text-anchor="middle" x="576" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
+</g>
+<!-- 32->29 -->
+<g id="edge50" class="edge">
+<title>32->29</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M601.4866,-503.8314C614.1659,-494.7927 629.6596,-483.7476 643.3055,-474.0198"/>
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+</g>
+<!-- 33->31 -->
+<g id="edge53" class="edge">
+<title>33->31</title>
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diff --git a/pipeline_documentation.md b/pipeline_documentation.md
index b34ee66b376c8193e8508101996ce24e346ffa27..0b22e0e02710c114274c4fba92a6b933e1882f6b 100644
--- a/pipeline_documentation.md
+++ b/pipeline_documentation.md
@@ -3,39 +3,36 @@ This document describes the individual rules of the pipeline for information pur
## Overview
### General
-* read samples table
-* create log directories
-* **create_index_star**
-* **extract_transcriptome**
-* **extract_decoys_salmon**
-* **concatenate_transcriptome_and_genome**
-* **create_index_salmon**
-* **create_index_kallisto**
-* **extract_transcripts_as_bed12**
-* **index_genomic_alignment_samtools**
-* **star_rpm**
-* **rename_star_rpm_for_alfa**
-* **calculate_TIN_scores**
-* **merge_TIN_scores**
-* **plot_TIN_scores**
-* **salmon_quantmerge_genes**
-* **salmon_quantmerge_transcripts**
-* **generate_alfa_index**
-* **alfa_qc**
-* **alfa_qc_all_samples**
-* **alfa_concat_results**
-* **prepare_files_for_report**
-* **prepare_MultiQC_config**
-* **MULTIQC_report**
+* [read samples table](#read-samples-table)
+* [create log directories](#create-log-directories)
+* **[create_index_star](#create_index_star)**
+* **[extract_transcriptome](#extract_transcriptome)**
+* **[create_index_salmon](#create_index_salmon)**
+* **[create_index_kallisto](#create_index_kallisto)**
+* **[extract_transcripts_as_bed12](#extract_transcripts_as_bed12)**
+* **[index_genomic_alignment_samtools](#index_genomic_alignment_samtools)**
+* **[star_rpm](#star_rpm)**
+* **[rename_star_rpm_for_alfa](#rename_star_rpm_for_alfa)**
+* **[calculate_TIN_scores](#calculate_TIN_scores)**
+* **[merge_TIN_scores](#merge_TIN_scores)**
+* **[plot_TIN_scores](#plot_TIN_scores)**
+* **[salmon_quantmerge_genes](#salmon_quantmerge_genes)**
+* **[salmon_quantmerge_transcripts](#salmon_quantmerge_transcripts)**
+* **[generate_alfa_index](#generate_alfa_index)**
+* **[alfa_qc](#alfa_qc)**
+* **[alfa_qc_all_samples](#alfa_qc_all_samples)**
+* **[prepare_files_for_report](#prepare_files_for_report)**
+* **[prepare_MultiQC_config](#prepare_MultiQC_config)**
+* **[MULTIQC_report](#MULTIQC_report)**
+* **[sort_bed_4_big](#sort_bed_4_big)**
### Sequencing mode specific
-* **(pe_)fastqc**
-* **(pe_)remove_adapters_cutadapt**
-* **(pe_)remove_polya_cutadapt**
-* **(pe_)map_genome_star**
-* **(pe_)quantification_salmon**
-* **(pe_)genome_quantification_kallisto**
-
+* **[(pe_)fastqc](#(pe_)fastqc)**
+* **[(pe_)remove_adapters_cutadapt](#(pe_)remove_adapters_cutadapt)**
+* **[(pe_)remove_polya_cutadapt](#(pe_)remove_polya_cutadapt)**
+* **[(pe_)map_genome_star](#(pe_)map_genome_star)**
+* **[(pe_)quantification_salmon](#(pe_)quantification_salmon)**
+* **[(pe_)genome_quantification_kallisto](#(pe_)genome_quantification_kallisto)**
@@ -100,23 +97,7 @@ Create transcriptome from genome and gene annotations using [gffread](https://gi
**Input:** `genome` and `gtf` of the input samples table
**Output:** transcriptome fasta file.
-
-#### extract_decoys_salmon
-Salmon indexing requires the names of the genome targets (https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/). Extract target names from the genome.
-
-
-**Input:** `genome` of the input samples table
-**Output:** text file with the genome targert names
-
-
-#### concatenate_transcriptome_and_genome
-Salmon indexing requires concatenated transcriptome and genome reference file (https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/).
-
-
-**Input:** `genome` of the input samples table and extracted transcriptome
-**Output:** fasta file with concatenated genome and transcriptome
-
-
+
#### create_index_salmon
Create index for [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html) quantification. Salmon index of transcriptome, required for mapping-based mode of Salmon. The index is created via an auxiliary k-mer hash over k-mers of length 31. While mapping algorithms will make use of arbitrarily long matches between the query and reference, the k-mer size selected here will act as the minimum acceptable length for a valid match. A k-mer size of 31 seems to work well for reads of 75bp or longer, although smaller size might improve sensitivity. A smaller k-mer size is suggested when working with shorter reads.
@@ -263,6 +244,18 @@ Interactive report of the various workflow steps. [MultiQC](https://multiqc.info
**Input:** Config file fort MultiQC in .yaml format
**Output:** Directory with automatically generated HTML report
+#### sort_bed_4_big
+Sorts bedgraph files for creating bigWig files. Using [bedtools sortBed](https://bedtools.readthedocs.io/en/latest/content/tools/sort.html)
+
+**Input:** bedgraph files from `rename_star_rpm_for_alfa`
+**Output:** sorted bedgraph files
+
+
+#### prepare_bigWig
+Check out some infos on bigWig files and [bedGraphtobigWig](http://genome.ucsc.edu/goldenPath/help/bigWig.html).
+
+**Input:** sorted bedgraph files, chromosome sizes from create_STAR_index
+**Output:** one bigWig file per sample and strand
### Sequencing mode specific rules
diff --git a/tests/test_integration_workflow/expected_output.files b/tests/test_integration_workflow/expected_output.files
index 796a9131b20194cca55d2ee7cf9789f62c9bcd7a..d2af64007b97a10a4add4389c63c44b0d87f21f6 100644
--- a/tests/test_integration_workflow/expected_output.files
+++ b/tests/test_integration_workflow/expected_output.files
@@ -16,66 +16,93 @@ results/star_indexes/homo_sapiens/75/STAR_index/sjdbInfo.txt
results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.fromGTF.out.tab
results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.out.tab
results/star_indexes/homo_sapiens/75/STAR_index/transcriptInfo.tab
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_adapters_mate1.fastq
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_adapters_mate2.fastq
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_polya_mate1.fastq
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_polya_mate2.fastq
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_SJ.out.tab
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/fastqc_data.txt
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/fastqc.fo
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/summary.txt
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/adapter_content.png
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/duplication_levels.png
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_n_content.png
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_quality.png
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_sequence_content.png
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_sequence_gc_content.png
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_sequence_quality.png
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_tile_quality.png
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/sequence_length_distribution.png
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/fastqc_data.txt
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/fastqc.fo
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/summary.txt
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/adapter_content.png
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/duplication_levels.png
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_base_n_content.png
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_base_quality.png
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_base_sequence_content.png
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_sequence_gc_content.png
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_sequence_quality.png
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_tile_quality.png
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/sequence_length_distribution.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_adapters_mate1.fastq
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_polya_mate1.fastq
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_adapters_mate2.fastq
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_polya_mate2.fastq
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.SJ.out.tab
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/fastqc_data.txt
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/fastqc.fo
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/summary.txt
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/fastqc_data.txt
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/fastqc.fo
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/summary.txt
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/adapter_content.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/duplication_levels.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_base_n_content.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_base_quality.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_base_sequence_content.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_sequence_gc_content.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_sequence_quality.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_tile_quality.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/sequence_length_distribution.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/adapter_content.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/duplication_levels.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_base_n_content.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_base_quality.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_base_sequence_content.png
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diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
index e3166e7cca1516315277f3ef2fc514b69e8c4b75..9d2e3a7a9d8e57fac141b063fa97a421923eb08f 100644
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