diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0b9cc4172ba3f10aa20bffa4e5fdfde066309f42..771bf2b488785040c83a37e005c1b7045da37bbb 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,7 +4,7 @@ before_script:
- apt update && apt install -y gcc
- conda init bash && source ~/.bashrc && echo $CONDA_DEFAULT_ENV
- conda env create -f install/environment.root.yml
- - conda activate rnaseq_pipeline && echo $CONDA_DEFAULT_ENV
+ - conda activate rhea && echo $CONDA_DEFAULT_ENV
- conda env update -f install/environment.dev.yml
test:
diff --git a/README.md b/README.md
index 3c966b4bc7e692737143b4ae67fa84adffbfe4fd..c4c32929964c49cd58de998e23f2e78fd1555ea6 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# RNA-Seq pipeline
+# Rhea pipeline
[Snakemake][snakemake] workflow for general purpose RNA-Seq library annotation
developed by the [Zavolan lab][zavolan-lab].
@@ -29,8 +29,8 @@ Traverse to the desired path on your file system, then clone the repository and
move into it with:
```bash
-git clone ssh://git@git.scicore.unibas.ch:2222/zavolan_group/pipelines/rnaseqpipeline.git
-cd rnaseqpipeline
+git clone ssh://git@git.scicore.unibas.ch:2222/zavolan_group/pipelines/rhea.git
+cd rhea
```
### Installing Conda
@@ -87,7 +87,7 @@ conda env create -f install/environment.root.yml
Activate the Conda environment with:
```bash
-conda activate rnaseq_pipeline
+conda activate rhea
```
### Installing non-essential dependencies
diff --git a/Snakefile b/Snakefile
index 97db0e37a7318235ecc8c990e8e94662a3d89e3b..c3b7de00130f733819cc7a340cb73bc70efc7301 100644
--- a/Snakefile
+++ b/Snakefile
@@ -5,6 +5,8 @@ import sys
import pandas as pd
import shutil
+import glob
+from zipfile import ZipFile
# Get sample table
samples_table = pd.read_csv(
@@ -17,7 +19,8 @@ samples_table = pd.read_csv(
)
# Global config
-localrules: finish, rename_star_rpm_for_alfa
+localrules: finish, rename_star_rpm_for_alfa, prepare_files_for_report, \
+ prepare_MultiQC_config
# Create log directories
os.makedirs(
@@ -44,76 +47,11 @@ rule finish:
Rule for collecting outputs
"""
input:
- outdir1 = expand(
- os.path.join(
- config['output_dir'],
- "{seqmode}",
- "{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)]),
- pseudoalignment = expand(
+ MultiQC_report = expand(
os.path.join(
config['output_dir'],
- "{seqmode}",
- "{sample}",
- "quant_kallisto",
- "{sample}.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"],
- "summary_salmon",
- "quantmerge",
- "genes_{salmon_merge_on}.tsv"),
- salmon_merge_on=["tpm", "numreads"]),
- salmon_merge_transcripts = expand(
- os.path.join(
- config["output_dir"],
- "summary_salmon",
- "quantmerge",
- "transcripts_{salmon_merge_on}.tsv"),
- salmon_merge_on=["tpm", "numreads"]),
- star_rpm = expand(
- os.path.join(
- config["output_dir"],
- "{seqmode}",
- "{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)]),
- alfa_reports = expand(os.path.join(
- config["output_dir"],
- "{seqmode}",
- "{sample}",
- "ALFA",
- "ALFA_plots.Biotypes.pdf"),
- 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)]),
- alfa_all_samples = os.path.join(
- config["output_dir"],
- "ALFA",
- "ALFA_plots.Categories.pdf")
-
-
-
+ "multiqc_summary"),
+ output_dir=config["output_dir"])
rule create_index_star:
"""
@@ -921,3 +859,377 @@ rule alfa_qc_all_samples:
"""
(alfa -c {input.tables} -o {params.out_dir}) &> {log}
"""
+
+
+rule prepare_files_for_report:
+ '''
+ Re-structure the results and add comments for MultiQC parsing
+ '''
+ input:
+ outdir1 = expand(
+ os.path.join(
+ config['output_dir'],
+ "{seqmode}",
+ "{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)]),
+ pseudoalignment = expand(
+ os.path.join(
+ config['output_dir'],
+ "{seqmode}",
+ "{sample}",
+ "quant_kallisto",
+ "{sample}.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"],
+ "summary_salmon",
+ "quantmerge",
+ "genes_{salmon_merge_on}.tsv"),
+ salmon_merge_on=["tpm", "numreads"]),
+ salmon_merge_transcripts = expand(
+ os.path.join(
+ config["output_dir"],
+ "summary_salmon",
+ "quantmerge",
+ "transcripts_{salmon_merge_on}.tsv"),
+ salmon_merge_on=["tpm", "numreads"]),
+ star_rpm = expand(
+ os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{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)]),
+ alfa_reports = expand(os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "ALFA",
+ "ALFA_plots.Biotypes.pdf"),
+ 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)]),
+ alfa_all_samples = os.path.join(
+ config["output_dir"],
+ "ALFA",
+ "ALFA_plots.Categories.pdf")
+
+ output:
+ samples_dir = directory(os.path.join(
+ "{output_dir}",
+ "samples"))
+ params:
+ results_dir = config["output_dir"],
+ log_dir = config["log_dir"],
+ log_samples_dir = os.path.join(
+ config["log_dir"],
+ "samples")
+ log:
+ LOG_local_log = \
+ os.path.join("{output_dir}", "local_log", \
+ "prepare_files_for_report.log")
+ run:
+
+ # remove "single/paired end" from the results directories
+ os.mkdir(output.samples_dir)
+ # move 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))
+ shutil.rmtree(
+ os.path.join(
+ params.results_dir,
+ "paired_end"),
+ ignore_errors=False,
+ onerror=None)
+ # move 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))
+ shutil.rmtree(
+ os.path.join(
+ params.results_dir,
+ "single_end"),
+ ignore_errors=False,
+ onerror=None)
+
+ # remove "single/paired end" from the logs directories
+ os.mkdir(params.log_samples_dir)
+ # move 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))
+ shutil.rmtree(
+ os.path.join(
+ params.log_dir,
+ "paired_end"),
+ ignore_errors=False,
+ onerror=None)
+ # move 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))
+ shutil.rmtree(
+ os.path.join(
+ params.log_dir,
+ "single_end"),
+ ignore_errors=False,
+ onerror=None)
+
+ # 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)
+ )
+
+ # 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]
+ zipfile_path_chunks = zipfile.split("/")
+ new_path = os.path.join(*(zipfile_path_chunks[:-1]))
+ with ZipFile(zipfile, 'r') as zip_f:
+ zip_f.extractall(new_path)
+ 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"))
+
+
+rule prepare_MultiQC_config:
+ '''
+ Prepare config for the MultiQC
+ '''
+ input:
+ multiqc_input_dir = os.path.join(
+ "{output_dir}",
+ "samples")
+ output:
+ multiqc_config = os.path.join(
+ "{output_dir}",
+ "MultiQC_config.yaml")
+ params:
+ logo_path = os.path.join(
+ "..",
+ "..",
+ "images",
+ "logo.128px.png"),
+ results_dir = config["output_dir"]
+ log:
+ LOG_local_log = \
+ os.path.join("{output_dir}", "local_log", \
+ "prepare_MultiQC_config.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(" - 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:
+ '''
+ Create report with MultiQC
+ '''
+ input:
+ multiqc_config = os.path.join(
+ config["output_dir"],
+ "MultiQC_config.yaml")
+ output:
+ MultiQC_report = \
+ directory(os.path.join("{output_dir}", "multiqc_summary"))
+ params:
+ results_dir = config["output_dir"],
+ log_dir = config["log_dir"]
+ log:
+ LOG_local_log = \
+ os.path.join("{output_dir}", "local_log", \
+ "MULTIQC_report.log")
+ singularity:
+ "docker://ewels/multiqc:1.7"
+ shell:
+ """
+ multiqc \
+ --outdir {output.MultiQC_report} \
+ --config {input.multiqc_config} \
+ {params.results_dir} \
+ {params.log_dir} \
+ &> {log.LOG_local_log};
+ """
\ No newline at end of file
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index 208139ab6dde973074b9b277c60d3f339b2cec89..1214e0a9721ab41108bc6d08150e6e12c5ba5179 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -4,514 +4,545 @@
<!-- Generated by graphviz version 2.38.0 (20140413.2041)
-->
<!-- Title: snakemake_dag Pages: 1 -->
-<svg width="1912pt" height="625pt"
- viewBox="0.00 0.00 1911.56 625.00" 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(4 621)">
+<svg width="1912pt" height="841pt"
+ viewBox="0.00 0.00 1911.56 841.00" 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(4 837)">
<title>snakemake_dag</title>
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+<polygon fill="white" stroke="none" points="-4,4 -4,-837 1907.56,-837 1907.56,4 -4,4"/>
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<g id="node1" class="node"><title>0</title>
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<text text-anchor="middle" x="1294" y="-15.5" font-family="sans" font-size="10.00">finish</text>
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-<text text-anchor="middle" x="146" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
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<g id="node4" class="node"><title>3</title>
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-<text text-anchor="middle" x="759" y="-159.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
+<path fill="none" stroke="#56a9d8" stroke-width="2" d="M1341.5,-252C1341.5,-252 1246.5,-252 1246.5,-252 1240.5,-252 1234.5,-246 1234.5,-240 1234.5,-240 1234.5,-228 1234.5,-228 1234.5,-222 1240.5,-216 1246.5,-216 1246.5,-216 1341.5,-216 1341.5,-216 1347.5,-216 1353.5,-222 1353.5,-228 1353.5,-228 1353.5,-240 1353.5,-240 1353.5,-246 1347.5,-252 1341.5,-252"/>
+<text text-anchor="middle" x="1294" y="-237" font-family="sans" font-size="10.00">prepare_files_for_report</text>
+<text text-anchor="middle" x="1294" y="-226" font-family="sans" font-size="10.00">output_dir: results</text>
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-<!-- 3->0 -->
-<g id="edge3" class="edge"><title>3->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M704.98,-143.962C688.226,-135.851 671.643,-124.258 662,-108 653.838,-94.2387 651.169,-83.777 662,-72 702.371,-28.1018 1127.09,-20.5458 1256.67,-19.2602"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1256.92,-22.7581 1266.89,-19.1659 1256.85,-15.7584 1256.92,-22.7581"/>
+<!-- 3->2 -->
+<g id="edge3" class="edge"><title>3->2</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1294,-215.697C1294,-207.983 1294,-198.712 1294,-190.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1297.5,-190.104 1294,-180.104 1290.5,-190.104 1297.5,-190.104"/>
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<!-- 4 -->
<g id="node5" class="node"><title>4</title>
-<path fill="none" stroke="#566bd8" stroke-width="2" d="M1273,-180C1273,-180 1147,-180 1147,-180 1141,-180 1135,-174 1135,-168 1135,-168 1135,-156 1135,-156 1135,-150 1141,-144 1147,-144 1147,-144 1273,-144 1273,-144 1279,-144 1285,-150 1285,-156 1285,-156 1285,-168 1285,-168 1285,-174 1279,-180 1273,-180"/>
-<text text-anchor="middle" x="1210" y="-159.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
+<path fill="none" stroke="#d85656" 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>
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-<!-- 4->0 -->
-<g id="edge4" class="edge"><title>4->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1280.09,-143.929C1298.08,-136.036 1315.35,-124.579 1326,-108 1338.64,-88.3232 1327.31,-62.9893 1314.77,-44.3855"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1317.49,-42.1755 1308.81,-36.1022 1311.81,-46.2637 1317.49,-42.1755"/>
+<!-- 4->3 -->
+<g id="edge4" class="edge"><title>4->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M292.011,-288.756C295.033,-288.494 298.032,-288.242 301,-288 646.799,-259.831 1061.61,-243.227 1223.99,-237.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1224.45,-240.876 1234.32,-237.021 1224.2,-233.88 1224.45,-240.876"/>
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<!-- 5 -->
<g id="node6" class="node"><title>5</title>
-<path fill="none" stroke="#56d873" stroke-width="2" d="M1462.5,-180C1462.5,-180 1397.5,-180 1397.5,-180 1391.5,-180 1385.5,-174 1385.5,-168 1385.5,-168 1385.5,-156 1385.5,-156 1385.5,-150 1391.5,-144 1397.5,-144 1397.5,-144 1462.5,-144 1462.5,-144 1468.5,-144 1474.5,-150 1474.5,-156 1474.5,-156 1474.5,-168 1474.5,-168 1474.5,-174 1468.5,-180 1462.5,-180"/>
-<text text-anchor="middle" x="1430" y="-159.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
+<path fill="none" stroke="#56d87b" 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>
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-<!-- 5->0 -->
-<g id="edge5" class="edge"><title>5->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1427.43,-143.676C1423.74,-124.193 1415.26,-92.5933 1397,-72 1379.42,-52.1643 1352.63,-38.7041 1330.79,-30.3127"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1331.74,-26.9356 1321.15,-26.8091 1329.35,-33.5145 1331.74,-26.9356"/>
+<!-- 5->3 -->
+<g id="edge5" class="edge"><title>5->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M614.408,-289.257C618.989,-288.827 623.528,-288.407 628,-288 845.188,-268.24 1102.6,-248.916 1224,-240.047"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1224.54,-243.516 1234.26,-239.298 1224.03,-236.535 1224.54,-243.516"/>
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<!-- 6 -->
<g id="node7" class="node"><title>6</title>
-<path fill="none" stroke="#56d882" stroke-width="2" d="M1141,-108C1141,-108 1029,-108 1029,-108 1023,-108 1017,-102 1017,-96 1017,-96 1017,-84 1017,-84 1017,-78 1023,-72 1029,-72 1029,-72 1141,-72 1141,-72 1147,-72 1153,-78 1153,-84 1153,-84 1153,-96 1153,-96 1153,-102 1147,-108 1141,-108"/>
-<text text-anchor="middle" x="1085" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
-<text text-anchor="middle" x="1085" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M830,-396C830,-396 688,-396 688,-396 682,-396 676,-390 676,-384 676,-384 676,-372 676,-372 676,-366 682,-360 688,-360 688,-360 830,-360 830,-360 836,-360 842,-366 842,-372 842,-372 842,-384 842,-384 842,-390 836,-396 830,-396"/>
+<text text-anchor="middle" x="759" y="-375.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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-<!-- 6->0 -->
-<g id="edge6" class="edge"><title>6->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1135.86,-71.9656C1173.31,-59.4227 1223.37,-42.6564 1257.05,-31.3763"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1258.57,-34.5572 1266.94,-28.0624 1256.35,-27.9196 1258.57,-34.5572"/>
+<!-- 6->3 -->
+<g id="edge6" class="edge"><title>6->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M704.98,-359.962C688.226,-351.851 671.643,-340.258 662,-324 653.838,-310.239 651.169,-299.777 662,-288 699.432,-247.298 1067.28,-237.839 1223.94,-235.652"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1224.44,-239.146 1234.39,-235.513 1224.35,-232.147 1224.44,-239.146"/>
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<!-- 7 -->
<g id="node8" class="node"><title>7</title>
-<path fill="none" stroke="#56d882" stroke-width="2" d="M1304.5,-108C1304.5,-108 1183.5,-108 1183.5,-108 1177.5,-108 1171.5,-102 1171.5,-96 1171.5,-96 1171.5,-84 1171.5,-84 1171.5,-78 1177.5,-72 1183.5,-72 1183.5,-72 1304.5,-72 1304.5,-72 1310.5,-72 1316.5,-78 1316.5,-84 1316.5,-84 1316.5,-96 1316.5,-96 1316.5,-102 1310.5,-108 1304.5,-108"/>
-<text text-anchor="middle" x="1244" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
-<text text-anchor="middle" x="1244" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M1273,-396C1273,-396 1147,-396 1147,-396 1141,-396 1135,-390 1135,-384 1135,-384 1135,-372 1135,-372 1135,-366 1141,-360 1147,-360 1147,-360 1273,-360 1273,-360 1279,-360 1285,-366 1285,-372 1285,-372 1285,-384 1285,-384 1285,-390 1279,-396 1273,-396"/>
+<text text-anchor="middle" x="1210" y="-375.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
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-<!-- 7->0 -->
-<g id="edge7" class="edge"><title>7->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1256.36,-71.6966C1262.23,-63.4741 1269.37,-53.4832 1275.84,-44.4207"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1278.82,-46.276 1281.78,-36.1043 1273.12,-42.2073 1278.82,-46.276"/>
+<!-- 7->3 -->
+<g id="edge7" class="edge"><title>7->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1280.09,-359.929C1298.08,-352.036 1315.35,-340.579 1326,-324 1338.64,-304.323 1327.31,-278.989 1314.77,-260.386"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1317.49,-258.175 1308.81,-252.102 1311.81,-262.264 1317.49,-258.175"/>
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<!-- 8 -->
<g id="node9" class="node"><title>8</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M813.5,-108C813.5,-108 682.5,-108 682.5,-108 676.5,-108 670.5,-102 670.5,-96 670.5,-96 670.5,-84 670.5,-84 670.5,-78 676.5,-72 682.5,-72 682.5,-72 813.5,-72 813.5,-72 819.5,-72 825.5,-78 825.5,-84 825.5,-84 825.5,-96 825.5,-96 825.5,-102 819.5,-108 813.5,-108"/>
-<text text-anchor="middle" x="748" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
-<text text-anchor="middle" x="748" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M1462.5,-396C1462.5,-396 1397.5,-396 1397.5,-396 1391.5,-396 1385.5,-390 1385.5,-384 1385.5,-384 1385.5,-372 1385.5,-372 1385.5,-366 1391.5,-360 1397.5,-360 1397.5,-360 1462.5,-360 1462.5,-360 1468.5,-360 1474.5,-366 1474.5,-372 1474.5,-372 1474.5,-384 1474.5,-384 1474.5,-390 1468.5,-396 1462.5,-396"/>
+<text text-anchor="middle" x="1430" y="-375.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
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-<!-- 8->0 -->
-<g id="edge8" class="edge"><title>8->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M825.735,-73.4985C828.861,-72.9741 831.958,-72.472 835,-72 990.957,-47.7965 1178.31,-29.4911 1256.68,-22.3138"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1257.36,-25.7666 1267,-21.3755 1256.72,-18.7954 1257.36,-25.7666"/>
+<!-- 8->3 -->
+<g id="edge8" class="edge"><title>8->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1427.43,-359.676C1423.74,-340.193 1415.26,-308.593 1397,-288 1385.29,-274.792 1369.5,-264.41 1353.81,-256.47"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1355.14,-253.228 1344.61,-252.074 1352.12,-259.544 1355.14,-253.228"/>
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<!-- 9 -->
<g id="node10" class="node"><title>9</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M986.5,-108C986.5,-108 855.5,-108 855.5,-108 849.5,-108 843.5,-102 843.5,-96 843.5,-96 843.5,-84 843.5,-84 843.5,-78 849.5,-72 855.5,-72 855.5,-72 986.5,-72 986.5,-72 992.5,-72 998.5,-78 998.5,-84 998.5,-84 998.5,-96 998.5,-96 998.5,-102 992.5,-108 986.5,-108"/>
-<text text-anchor="middle" x="921" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
-<text text-anchor="middle" x="921" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
+<path fill="none" stroke="#568ad8" stroke-width="2" d="M1141,-324C1141,-324 1029,-324 1029,-324 1023,-324 1017,-318 1017,-312 1017,-312 1017,-300 1017,-300 1017,-294 1023,-288 1029,-288 1029,-288 1141,-288 1141,-288 1147,-288 1153,-294 1153,-300 1153,-300 1153,-312 1153,-312 1153,-318 1147,-324 1141,-324"/>
+<text text-anchor="middle" x="1085" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="1085" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
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-<!-- 9->0 -->
-<g id="edge9" class="edge"><title>9->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M998.781,-73.7625C1001.89,-73.165 1004.98,-72.5756 1008,-72 1097.25,-55.0116 1202.3,-35.7258 1256.87,-25.7615"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1257.56,-29.1926 1266.77,-23.9542 1256.31,-22.3063 1257.56,-29.1926"/>
+<!-- 9->3 -->
+<g id="edge9" class="edge"><title>9->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1135.86,-287.966C1165.19,-278.142 1202.25,-265.729 1233.12,-255.389"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1234.54,-258.606 1242.91,-252.111 1232.32,-251.968 1234.54,-258.606"/>
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<!-- 10 -->
<g id="node11" class="node"><title>10</title>
-<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1358.5,-324C1358.5,-324 1327.5,-324 1327.5,-324 1321.5,-324 1315.5,-318 1315.5,-312 1315.5,-312 1315.5,-300 1315.5,-300 1315.5,-294 1321.5,-288 1327.5,-288 1327.5,-288 1358.5,-288 1358.5,-288 1364.5,-288 1370.5,-294 1370.5,-300 1370.5,-300 1370.5,-312 1370.5,-312 1370.5,-318 1364.5,-324 1358.5,-324"/>
-<text text-anchor="middle" x="1343" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
+<path fill="none" stroke="#568ad8" stroke-width="2" d="M1304.5,-324C1304.5,-324 1183.5,-324 1183.5,-324 1177.5,-324 1171.5,-318 1171.5,-312 1171.5,-312 1171.5,-300 1171.5,-300 1171.5,-294 1177.5,-288 1183.5,-288 1183.5,-288 1304.5,-288 1304.5,-288 1310.5,-288 1316.5,-294 1316.5,-300 1316.5,-300 1316.5,-312 1316.5,-312 1316.5,-318 1310.5,-324 1304.5,-324"/>
+<text text-anchor="middle" x="1244" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="1244" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
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-<!-- 10->0 -->
-<g id="edge10" class="edge"><title>10->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1346.95,-287.853C1355.25,-248.209 1371.41,-147.802 1342,-72 1337.87,-61.3668 1330.53,-51.5395 1322.8,-43.3091"/>
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-<!-- 25 -->
-<g id="node26" class="node"><title>25</title>
-<path fill="none" stroke="#d87d56" stroke-width="2" d="M1489,-252C1489,-252 1383,-252 1383,-252 1377,-252 1371,-246 1371,-240 1371,-240 1371,-228 1371,-228 1371,-222 1377,-216 1383,-216 1383,-216 1489,-216 1489,-216 1495,-216 1501,-222 1501,-228 1501,-228 1501,-240 1501,-240 1501,-246 1495,-252 1489,-252"/>
-<text text-anchor="middle" x="1436" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
-</g>
-<!-- 10->25 -->
-<g id="edge53" class="edge"><title>10->25</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1365.99,-287.697C1377.81,-278.796 1392.39,-267.823 1405.18,-258.199"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1407.39,-260.915 1413.28,-252.104 1403.18,-255.322 1407.39,-260.915"/>
+<!-- 10->3 -->
+<g id="edge10" class="edge"><title>10->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1256.36,-287.697C1262.23,-279.474 1269.37,-269.483 1275.84,-260.421"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1278.82,-262.276 1281.78,-252.104 1273.12,-258.207 1278.82,-262.276"/>
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<!-- 11 -->
<g id="node12" class="node"><title>11</title>
-<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1863.5,-324C1863.5,-324 1832.5,-324 1832.5,-324 1826.5,-324 1820.5,-318 1820.5,-312 1820.5,-312 1820.5,-300 1820.5,-300 1820.5,-294 1826.5,-288 1832.5,-288 1832.5,-288 1863.5,-288 1863.5,-288 1869.5,-288 1875.5,-294 1875.5,-300 1875.5,-300 1875.5,-312 1875.5,-312 1875.5,-318 1869.5,-324 1863.5,-324"/>
-<text text-anchor="middle" x="1848" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
+<path fill="none" stroke="#567bd8" stroke-width="2" d="M813.5,-324C813.5,-324 682.5,-324 682.5,-324 676.5,-324 670.5,-318 670.5,-312 670.5,-312 670.5,-300 670.5,-300 670.5,-294 676.5,-288 682.5,-288 682.5,-288 813.5,-288 813.5,-288 819.5,-288 825.5,-294 825.5,-300 825.5,-300 825.5,-312 825.5,-312 825.5,-318 819.5,-324 813.5,-324"/>
+<text text-anchor="middle" x="748" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="748" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
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-<!-- 11->0 -->
-<g id="edge11" class="edge"><title>11->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1870.6,-287.963C1881.06,-278.635 1892.4,-266.107 1898,-252 1903.91,-237.13 1906.17,-229.758 1898,-216 1829.77,-101.072 1760.57,-114.929 1634,-72 1528.11,-36.0846 1395.31,-24.3556 1331.55,-20.6448"/>
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-<g id="node28" class="node"><title>27</title>
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-<text text-anchor="middle" x="1824" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
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-<!-- 11->27 -->
-<g id="edge55" class="edge"><title>11->27</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1836.42,-260.429 1829.86,-252.104 1829.8,-262.699 1836.42,-260.429"/>
+<!-- 11->3 -->
+<g id="edge11" class="edge"><title>11->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M825.735,-289.499C828.861,-288.974 831.958,-288.472 835,-288 972.388,-266.678 1134.14,-249.934 1224.29,-241.342"/>
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<!-- 12 -->
<g id="node13" class="node"><title>12</title>
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-<text text-anchor="middle" x="1534" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
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-<!-- 12->0 -->
-<g id="edge12" class="edge"><title>12->0</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1331.62,-27.91 1321.03,-27.8593 1329.28,-34.5059 1331.62,-27.91"/>
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-<!-- 14 -->
-<g id="node15" class="node"><title>14</title>
-<path fill="none" stroke="#d8c356" stroke-width="2" d="M1580.5,-108C1580.5,-108 1499.5,-108 1499.5,-108 1493.5,-108 1487.5,-102 1487.5,-96 1487.5,-96 1487.5,-84 1487.5,-84 1487.5,-78 1493.5,-72 1499.5,-72 1499.5,-72 1580.5,-72 1580.5,-72 1586.5,-72 1592.5,-78 1592.5,-84 1592.5,-84 1592.5,-96 1592.5,-96 1592.5,-102 1586.5,-108 1580.5,-108"/>
-<text text-anchor="middle" x="1540" y="-87.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
+<path fill="none" stroke="#567bd8" stroke-width="2" d="M986.5,-324C986.5,-324 855.5,-324 855.5,-324 849.5,-324 843.5,-318 843.5,-312 843.5,-312 843.5,-300 843.5,-300 843.5,-294 849.5,-288 855.5,-288 855.5,-288 986.5,-288 986.5,-288 992.5,-288 998.5,-294 998.5,-300 998.5,-300 998.5,-312 998.5,-312 998.5,-318 992.5,-324 986.5,-324"/>
+<text text-anchor="middle" x="921" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="921" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
</g>
-<!-- 12->14 -->
-<g id="edge36" class="edge"><title>12->14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1535.48,-143.697C1536.14,-135.983 1536.94,-126.712 1537.68,-118.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1541.17,-118.367 1538.53,-108.104 1534.19,-117.769 1541.17,-118.367"/>
+<!-- 12->3 -->
+<g id="edge12" class="edge"><title>12->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M998.781,-289.763C1001.89,-289.165 1004.98,-288.576 1008,-288 1081.71,-273.97 1166.2,-258.372 1224.12,-247.753"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1225.06,-251.141 1234.26,-245.896 1223.79,-244.255 1225.06,-251.141"/>
</g>
<!-- 13 -->
<g id="node14" class="node"><title>13</title>
-<path fill="none" stroke="#56d85b" stroke-width="2" d="M1684,-180C1684,-180 1654,-180 1654,-180 1648,-180 1642,-174 1642,-168 1642,-168 1642,-156 1642,-156 1642,-150 1648,-144 1654,-144 1654,-144 1684,-144 1684,-144 1690,-144 1696,-150 1696,-156 1696,-156 1696,-168 1696,-168 1696,-174 1690,-180 1684,-180"/>
-<text text-anchor="middle" x="1669" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1358.5,-540C1358.5,-540 1327.5,-540 1327.5,-540 1321.5,-540 1315.5,-534 1315.5,-528 1315.5,-528 1315.5,-516 1315.5,-516 1315.5,-510 1321.5,-504 1327.5,-504 1327.5,-504 1358.5,-504 1358.5,-504 1364.5,-504 1370.5,-510 1370.5,-516 1370.5,-516 1370.5,-528 1370.5,-528 1370.5,-534 1364.5,-540 1358.5,-540"/>
+<text text-anchor="middle" x="1343" y="-519.5" font-family="sans" font-size="10.00">star_rpm</text>
+</g>
+<!-- 13->3 -->
+<g id="edge13" class="edge"><title>13->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1346.95,-503.853C1355.25,-464.209 1371.41,-363.802 1342,-288 1337.87,-277.367 1330.53,-267.54 1322.8,-259.309"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1325.24,-256.797 1315.68,-252.222 1320.3,-261.758 1325.24,-256.797"/>
</g>
-<!-- 13->0 -->
-<g id="edge13" class="edge"><title>13->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1661.08,-143.778C1650.64,-123.151 1630.23,-89.2286 1602,-72 1557.07,-44.5771 1403.3,-28.2763 1331.5,-21.9921"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1331.38,-18.4689 1321.11,-21.1033 1330.78,-25.4434 1331.38,-18.4689"/>
+<!-- 28 -->
+<g id="node29" class="node"><title>28</title>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M1489,-468C1489,-468 1383,-468 1383,-468 1377,-468 1371,-462 1371,-456 1371,-456 1371,-444 1371,-444 1371,-438 1377,-432 1383,-432 1383,-432 1489,-432 1489,-432 1495,-432 1501,-438 1501,-444 1501,-444 1501,-456 1501,-456 1501,-462 1495,-468 1489,-468"/>
+<text text-anchor="middle" x="1436" y="-447.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
</g>
-<!-- 13->14 -->
-<g id="edge37" class="edge"><title>13->14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1641.96,-146.326C1624.15,-136.661 1600.5,-123.831 1580.47,-112.96"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1582.01,-109.815 1571.55,-108.122 1578.67,-115.968 1582.01,-109.815"/>
+<!-- 13->28 -->
+<g id="edge56" class="edge"><title>13->28</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1365.99,-503.697C1377.81,-494.796 1392.39,-483.823 1405.18,-474.199"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1407.39,-476.915 1413.28,-468.104 1403.18,-471.322 1407.39,-476.915"/>
</g>
-<!-- 14->0 -->
-<g id="edge14" class="edge"><title>14->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1487.23,-73.9832C1440.14,-60.5856 1372.41,-41.3131 1330.91,-29.5036"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1331.78,-26.1127 1321.21,-26.7421 1329.87,-32.8454 1331.78,-26.1127"/>
+<!-- 14 -->
+<g id="node15" class="node"><title>14</title>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1863.5,-540C1863.5,-540 1832.5,-540 1832.5,-540 1826.5,-540 1820.5,-534 1820.5,-528 1820.5,-528 1820.5,-516 1820.5,-516 1820.5,-510 1826.5,-504 1832.5,-504 1832.5,-504 1863.5,-504 1863.5,-504 1869.5,-504 1875.5,-510 1875.5,-516 1875.5,-516 1875.5,-528 1875.5,-528 1875.5,-534 1869.5,-540 1863.5,-540"/>
+<text text-anchor="middle" x="1848" y="-519.5" font-family="sans" font-size="10.00">star_rpm</text>
+</g>
+<!-- 14->3 -->
+<g id="edge14" class="edge"><title>14->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1870.6,-503.963C1881.06,-494.635 1892.4,-482.107 1898,-468 1903.91,-453.13 1906.17,-445.758 1898,-432 1829.77,-317.072 1760.57,-330.929 1634,-288 1543.54,-257.32 1433.45,-244.289 1363.54,-238.829"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1363.76,-235.335 1353.52,-238.077 1363.23,-242.316 1363.76,-235.335"/>
+</g>
+<!-- 30 -->
+<g id="node31" class="node"><title>30</title>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M1877,-468C1877,-468 1771,-468 1771,-468 1765,-468 1759,-462 1759,-456 1759,-456 1759,-444 1759,-444 1759,-438 1765,-432 1771,-432 1771,-432 1877,-432 1877,-432 1883,-432 1889,-438 1889,-444 1889,-444 1889,-456 1889,-456 1889,-462 1883,-468 1877,-468"/>
+<text text-anchor="middle" x="1824" y="-447.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
+</g>
+<!-- 14->30 -->
+<g id="edge58" class="edge"><title>14->30</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1842.07,-503.697C1839.39,-495.898 1836.17,-486.509 1833.2,-477.829"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1836.42,-476.429 1829.86,-468.104 1829.8,-478.699 1836.42,-476.429"/>
</g>
<!-- 15 -->
<g id="node16" class="node"><title>15</title>
-<path fill="none" stroke="#568ad8" stroke-width="2" d="M916,-542.5C916,-542.5 804,-542.5 804,-542.5 798,-542.5 792,-536.5 792,-530.5 792,-530.5 792,-518.5 792,-518.5 792,-512.5 798,-506.5 804,-506.5 804,-506.5 916,-506.5 916,-506.5 922,-506.5 928,-512.5 928,-518.5 928,-518.5 928,-530.5 928,-530.5 928,-536.5 922,-542.5 916,-542.5"/>
-<text text-anchor="middle" x="860" y="-522" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+<path fill="none" stroke="#569ad8" stroke-width="2" d="M1549,-396C1549,-396 1519,-396 1519,-396 1513,-396 1507,-390 1507,-384 1507,-384 1507,-372 1507,-372 1507,-366 1513,-360 1519,-360 1519,-360 1549,-360 1549,-360 1555,-360 1561,-366 1561,-372 1561,-372 1561,-384 1561,-384 1561,-390 1555,-396 1549,-396"/>
+<text text-anchor="middle" x="1534" y="-375.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
<!-- 15->3 -->
<g id="edge15" class="edge"><title>15->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M845.155,-506.122C824.607,-480.23 790,-429.176 790,-379 790,-379 790,-379 790,-305 790,-264.098 777.572,-218.063 768.454,-189.793"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="771.749,-188.61 765.273,-180.224 765.106,-190.817 771.749,-188.61"/>
-</g>
-<!-- 19 -->
-<g id="node20" class="node"><title>19</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M975.5,-180C975.5,-180 872.5,-180 872.5,-180 866.5,-180 860.5,-174 860.5,-168 860.5,-168 860.5,-156 860.5,-156 860.5,-150 866.5,-144 872.5,-144 872.5,-144 975.5,-144 975.5,-144 981.5,-144 987.5,-150 987.5,-156 987.5,-156 987.5,-168 987.5,-168 987.5,-174 981.5,-180 975.5,-180"/>
-<text text-anchor="middle" x="924" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
-</g>
-<!-- 15->19 -->
-<g id="edge43" class="edge"><title>15->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M860,-506.151C860,-479.022 860,-424.909 860,-379 860,-379 860,-379 860,-305 860,-264.458 862.112,-252.382 880,-216 884.958,-205.915 892.205,-196.093 899.392,-187.699"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="902.113,-189.907 906.188,-180.127 896.904,-185.232 902.113,-189.907"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1515.56,-359.869C1494.09,-340.564 1456.96,-309.127 1421,-288 1399.74,-275.506 1374.97,-264.471 1352.99,-255.749"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1354.02,-252.395 1343.43,-252.032 1351.48,-258.919 1354.02,-252.395"/>
</g>
-<!-- 21 -->
-<g id="node22" class="node"><title>21</title>
-<path fill="none" stroke="#d8d356" stroke-width="2" d="M1387.5,-468C1387.5,-468 1298.5,-468 1298.5,-468 1292.5,-468 1286.5,-462 1286.5,-456 1286.5,-456 1286.5,-444 1286.5,-444 1286.5,-438 1292.5,-432 1298.5,-432 1298.5,-432 1387.5,-432 1387.5,-432 1393.5,-432 1399.5,-438 1399.5,-444 1399.5,-444 1399.5,-456 1399.5,-456 1399.5,-462 1393.5,-468 1387.5,-468"/>
-<text text-anchor="middle" x="1343" y="-447.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+<!-- 17 -->
+<g id="node18" class="node"><title>17</title>
+<path fill="none" stroke="#56d863" stroke-width="2" d="M1580.5,-324C1580.5,-324 1499.5,-324 1499.5,-324 1493.5,-324 1487.5,-318 1487.5,-312 1487.5,-312 1487.5,-300 1487.5,-300 1487.5,-294 1493.5,-288 1499.5,-288 1499.5,-288 1580.5,-288 1580.5,-288 1586.5,-288 1592.5,-294 1592.5,-300 1592.5,-300 1592.5,-312 1592.5,-312 1592.5,-318 1586.5,-324 1580.5,-324"/>
+<text text-anchor="middle" x="1540" y="-303.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
</g>
-<!-- 15->21 -->
-<g id="edge48" class="edge"><title>15->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M928.178,-513.266C1020.66,-499.384 1184.83,-474.742 1276.46,-460.988"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1277.08,-464.433 1286.45,-459.488 1276.05,-457.511 1277.08,-464.433"/>
+<!-- 15->17 -->
+<g id="edge39" class="edge"><title>15->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1535.48,-359.697C1536.14,-351.983 1536.94,-342.712 1537.68,-334.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1541.17,-334.367 1538.53,-324.104 1534.19,-333.769 1541.17,-334.367"/>
</g>
<!-- 16 -->
<g id="node17" class="node"><title>16</title>
-<path fill="none" stroke="#d8ac56" stroke-width="2" d="M1112,-252C1112,-252 1028,-252 1028,-252 1022,-252 1016,-246 1016,-240 1016,-240 1016,-228 1016,-228 1016,-222 1022,-216 1028,-216 1028,-216 1112,-216 1112,-216 1118,-216 1124,-222 1124,-228 1124,-228 1124,-240 1124,-240 1124,-246 1118,-252 1112,-252"/>
-<text text-anchor="middle" x="1070" y="-231.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+<path fill="none" stroke="#569ad8" stroke-width="2" d="M1684,-396C1684,-396 1654,-396 1654,-396 1648,-396 1642,-390 1642,-384 1642,-384 1642,-372 1642,-372 1642,-366 1648,-360 1654,-360 1654,-360 1684,-360 1684,-360 1690,-360 1696,-366 1696,-372 1696,-372 1696,-384 1696,-384 1696,-390 1690,-396 1684,-396"/>
+<text text-anchor="middle" x="1669" y="-375.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
<!-- 16->3 -->
<g id="edge16" class="edge"><title>16->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1015.75,-218.165C1012.79,-217.418 1009.86,-216.692 1007,-216 956.065,-203.694 898.887,-191.375 852.28,-181.715"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="852.7,-178.228 842.199,-179.632 851.284,-185.083 852.7,-178.228"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1661.08,-359.778C1650.64,-339.151 1630.23,-305.229 1602,-288 1563.05,-264.229 1442.32,-248.815 1364.09,-241.038"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1364.12,-237.524 1353.83,-240.037 1363.44,-244.491 1364.12,-237.524"/>
</g>
-<!-- 16->4 -->
-<g id="edge18" class="edge"><title>16->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1104.25,-215.876C1123.06,-206.469 1146.58,-194.708 1166.67,-184.667"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1168.24,-187.792 1175.62,-180.19 1165.11,-181.531 1168.24,-187.792"/>
+<!-- 16->17 -->
+<g id="edge40" class="edge"><title>16->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1641.96,-362.326C1624.15,-352.661 1600.5,-339.831 1580.47,-328.96"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1582.01,-325.815 1571.55,-324.122 1578.67,-331.968 1582.01,-325.815"/>
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-<!-- 17 -->
-<g id="node18" class="node"><title>17</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1238,-542.5C1238,-542.5 1142,-542.5 1142,-542.5 1136,-542.5 1130,-536.5 1130,-530.5 1130,-530.5 1130,-518.5 1130,-518.5 1130,-512.5 1136,-506.5 1142,-506.5 1142,-506.5 1238,-506.5 1238,-506.5 1244,-506.5 1250,-512.5 1250,-518.5 1250,-518.5 1250,-530.5 1250,-530.5 1250,-536.5 1244,-542.5 1238,-542.5"/>
-<text text-anchor="middle" x="1190" y="-522" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
+<!-- 17->3 -->
+<g id="edge17" class="edge"><title>17->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1487.23,-289.983C1451.05,-279.688 1402.67,-265.923 1363.38,-254.742"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1364.17,-251.329 1353.6,-251.958 1362.26,-258.062 1364.17,-251.329"/>
</g>
-<!-- 17->4 -->
-<g id="edge17" class="edge"><title>17->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1190,-506.151C1190,-479.022 1190,-424.909 1190,-379 1190,-379 1190,-379 1190,-305 1190,-264.822 1197.95,-218.869 1203.82,-190.389"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1207.3,-190.887 1205.95,-180.378 1200.45,-189.431 1207.3,-190.887"/>
+<!-- 18 -->
+<g id="node19" class="node"><title>18</title>
+<path fill="none" stroke="#d87556" stroke-width="2" d="M916,-758.5C916,-758.5 804,-758.5 804,-758.5 798,-758.5 792,-752.5 792,-746.5 792,-746.5 792,-734.5 792,-734.5 792,-728.5 798,-722.5 804,-722.5 804,-722.5 916,-722.5 916,-722.5 922,-722.5 928,-728.5 928,-734.5 928,-734.5 928,-746.5 928,-746.5 928,-752.5 922,-758.5 916,-758.5"/>
+<text text-anchor="middle" x="860" y="-738" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
-<!-- 20 -->
-<g id="node21" class="node"><title>20</title>
-<path fill="none" stroke="#d89c56" stroke-width="2" d="M1104.5,-180C1104.5,-180 1017.5,-180 1017.5,-180 1011.5,-180 1005.5,-174 1005.5,-168 1005.5,-168 1005.5,-156 1005.5,-156 1005.5,-150 1011.5,-144 1017.5,-144 1017.5,-144 1104.5,-144 1104.5,-144 1110.5,-144 1116.5,-150 1116.5,-156 1116.5,-156 1116.5,-168 1116.5,-168 1116.5,-174 1110.5,-180 1104.5,-180"/>
-<text text-anchor="middle" x="1061" y="-159.5" font-family="sans" font-size="10.00">quantification_salmon</text>
+<!-- 18->6 -->
+<g id="edge18" class="edge"><title>18->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M845.155,-722.122C824.607,-696.23 790,-645.176 790,-595 790,-595 790,-595 790,-521 790,-480.098 777.572,-434.063 768.454,-405.793"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="771.749,-404.61 765.273,-396.224 765.106,-406.817 771.749,-404.61"/>
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-<!-- 17->20 -->
-<g id="edge45" class="edge"><title>17->20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1182.31,-506.093C1171.21,-479.328 1152,-426.21 1152,-379 1152,-379 1152,-379 1152,-305 1152,-264.553 1154.94,-249.98 1133,-216 1125.28,-204.038 1113.84,-193.843 1102.35,-185.685"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1104.28,-182.765 1094.02,-180.109 1100.39,-188.581 1104.28,-182.765"/>
+<!-- 22 -->
+<g id="node23" class="node"><title>22</title>
+<path fill="none" stroke="#d89556" stroke-width="2" d="M975.5,-396C975.5,-396 872.5,-396 872.5,-396 866.5,-396 860.5,-390 860.5,-384 860.5,-384 860.5,-372 860.5,-372 860.5,-366 866.5,-360 872.5,-360 872.5,-360 975.5,-360 975.5,-360 981.5,-360 987.5,-366 987.5,-372 987.5,-372 987.5,-384 987.5,-384 987.5,-390 981.5,-396 975.5,-396"/>
+<text text-anchor="middle" x="924" y="-375.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
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-<!-- 23 -->
-<g id="node24" class="node"><title>23</title>
-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M1753.5,-468C1753.5,-468 1680.5,-468 1680.5,-468 1674.5,-468 1668.5,-462 1668.5,-456 1668.5,-456 1668.5,-444 1668.5,-444 1668.5,-438 1674.5,-432 1680.5,-432 1680.5,-432 1753.5,-432 1753.5,-432 1759.5,-432 1765.5,-438 1765.5,-444 1765.5,-444 1765.5,-456 1765.5,-456 1765.5,-462 1759.5,-468 1753.5,-468"/>
-<text text-anchor="middle" x="1717" y="-447.5" font-family="sans" font-size="10.00">map_genome_star</text>
+<!-- 18->22 -->
+<g id="edge46" class="edge"><title>18->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M860,-722.151C860,-695.022 860,-640.909 860,-595 860,-595 860,-595 860,-521 860,-480.458 862.112,-468.382 880,-432 884.958,-421.915 892.205,-412.093 899.392,-403.699"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="902.113,-405.907 906.188,-396.127 896.904,-401.232 902.113,-405.907"/>
</g>
-<!-- 17->23 -->
-<g id="edge51" class="edge"><title>17->23</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1250.2,-515.219C1352.16,-501.192 1557.56,-472.934 1658.42,-459.059"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1659,-462.512 1668.43,-457.682 1658.05,-455.577 1659,-462.512"/>
+<!-- 24 -->
+<g id="node25" class="node"><title>24</title>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1387.5,-684C1387.5,-684 1298.5,-684 1298.5,-684 1292.5,-684 1286.5,-678 1286.5,-672 1286.5,-672 1286.5,-660 1286.5,-660 1286.5,-654 1292.5,-648 1298.5,-648 1298.5,-648 1387.5,-648 1387.5,-648 1393.5,-648 1399.5,-654 1399.5,-660 1399.5,-660 1399.5,-672 1399.5,-672 1399.5,-678 1393.5,-684 1387.5,-684"/>
+<text text-anchor="middle" x="1343" y="-663.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
</g>
-<!-- 18 -->
-<g id="node19" class="node"><title>18</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1607,-252C1607,-252 1531,-252 1531,-252 1525,-252 1519,-246 1519,-240 1519,-240 1519,-228 1519,-228 1519,-222 1525,-216 1531,-216 1531,-216 1607,-216 1607,-216 1613,-216 1619,-222 1619,-228 1619,-228 1619,-240 1619,-240 1619,-246 1613,-252 1607,-252"/>
-<text text-anchor="middle" x="1569" y="-231.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
+<!-- 18->24 -->
+<g id="edge51" class="edge"><title>18->24</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M928.178,-729.266C1020.66,-715.384 1184.83,-690.742 1276.46,-676.988"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1277.08,-680.433 1286.45,-675.488 1276.05,-673.511 1277.08,-680.433"/>
</g>
-<!-- 18->5 -->
-<g id="edge19" class="edge"><title>18->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1535,-215.876C1516.4,-206.512 1493.17,-194.814 1473.29,-184.803"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1474.64,-181.562 1464.13,-180.19 1471.49,-187.814 1474.64,-181.562"/>
+<!-- 19 -->
+<g id="node20" class="node"><title>19</title>
+<path fill="none" stroke="#68d856" stroke-width="2" d="M1112,-468C1112,-468 1028,-468 1028,-468 1022,-468 1016,-462 1016,-456 1016,-456 1016,-444 1016,-444 1016,-438 1022,-432 1028,-432 1028,-432 1112,-432 1112,-432 1118,-432 1124,-438 1124,-444 1124,-444 1124,-456 1124,-456 1124,-462 1118,-468 1112,-468"/>
+<text text-anchor="middle" x="1070" y="-447.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
</g>
<!-- 19->6 -->
-<g id="edge20" class="edge"><title>19->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M963.385,-143.876C985.395,-134.307 1013.01,-122.3 1036.36,-112.148"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1037.97,-115.265 1045.74,-108.068 1035.18,-108.846 1037.97,-115.265"/>
+<g id="edge19" class="edge"><title>19->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1015.75,-434.165C1012.79,-433.418 1009.86,-432.692 1007,-432 956.065,-419.694 898.887,-407.375 852.28,-397.715"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="852.7,-394.228 842.199,-395.632 851.284,-401.083 852.7,-394.228"/>
</g>
<!-- 19->7 -->
-<g id="edge22" class="edge"><title>19->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M987.686,-146.1C990.834,-145.385 993.952,-144.682 997,-144 1051.64,-131.776 1113.21,-118.563 1161.21,-108.387"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1162.19,-111.759 1171.24,-106.264 1160.74,-104.911 1162.19,-111.759"/>
-</g>
-<!-- 19->8 -->
-<g id="edge24" class="edge"><title>19->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M880.946,-143.876C856.671,-134.222 826.16,-122.087 800.492,-111.878"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="801.5,-108.512 790.915,-108.068 798.913,-115.016 801.5,-108.512"/>
-</g>
-<!-- 19->9 -->
-<g id="edge26" class="edge"><title>19->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M923.258,-143.697C922.928,-135.983 922.531,-126.712 922.162,-118.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="925.658,-117.945 921.733,-108.104 918.665,-118.245 925.658,-117.945"/>
+<g id="edge21" class="edge"><title>19->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1104.25,-431.876C1123.06,-422.469 1146.58,-410.708 1166.67,-400.667"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1168.24,-403.792 1175.62,-396.19 1165.11,-397.531 1168.24,-403.792"/>
</g>
-<!-- 20->6 -->
-<g id="edge21" class="edge"><title>20->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1066.93,-143.697C1069.61,-135.898 1072.83,-126.509 1075.8,-117.829"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1079.2,-118.699 1079.14,-108.104 1072.58,-116.429 1079.2,-118.699"/>
+<!-- 20 -->
+<g id="node21" class="node"><title>20</title>
+<path fill="none" stroke="#56d8d8" stroke-width="2" d="M1238,-758.5C1238,-758.5 1142,-758.5 1142,-758.5 1136,-758.5 1130,-752.5 1130,-746.5 1130,-746.5 1130,-734.5 1130,-734.5 1130,-728.5 1136,-722.5 1142,-722.5 1142,-722.5 1238,-722.5 1238,-722.5 1244,-722.5 1250,-728.5 1250,-734.5 1250,-734.5 1250,-746.5 1250,-746.5 1250,-752.5 1244,-758.5 1238,-758.5"/>
+<text text-anchor="middle" x="1190" y="-738" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
<!-- 20->7 -->
-<g id="edge23" class="edge"><title>20->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1105.77,-143.876C1131.12,-134.179 1163.01,-121.98 1189.77,-111.743"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1191.29,-114.91 1199.38,-108.068 1188.79,-108.372 1191.29,-114.91"/>
+<g id="edge20" class="edge"><title>20->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1190,-722.151C1190,-695.022 1190,-640.909 1190,-595 1190,-595 1190,-595 1190,-521 1190,-480.822 1197.95,-434.869 1203.82,-406.389"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1207.3,-406.887 1205.95,-396.378 1200.45,-405.431 1207.3,-406.887"/>
</g>
-<!-- 20->8 -->
-<g id="edge25" class="edge"><title>20->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1005.19,-146.001C1002.43,-145.312 999.684,-144.642 997,-144 943.625,-131.239 883.449,-118.389 835.625,-108.537"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="836.114,-105.065 825.615,-106.482 834.706,-111.922 836.114,-105.065"/>
+<!-- 23 -->
+<g id="node24" class="node"><title>23</title>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1104.5,-396C1104.5,-396 1017.5,-396 1017.5,-396 1011.5,-396 1005.5,-390 1005.5,-384 1005.5,-384 1005.5,-372 1005.5,-372 1005.5,-366 1011.5,-360 1017.5,-360 1017.5,-360 1104.5,-360 1104.5,-360 1110.5,-360 1116.5,-366 1116.5,-372 1116.5,-372 1116.5,-384 1116.5,-384 1116.5,-390 1110.5,-396 1104.5,-396"/>
+<text text-anchor="middle" x="1061" y="-375.5" font-family="sans" font-size="10.00">quantification_salmon</text>
</g>
-<!-- 20->9 -->
-<g id="edge27" class="edge"><title>20->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1026.75,-143.876C1007.94,-134.469 984.415,-122.708 964.334,-112.667"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="965.889,-109.531 955.38,-108.19 962.759,-115.792 965.889,-109.531"/>
+<!-- 20->23 -->
+<g id="edge48" class="edge"><title>20->23</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1182.31,-722.093C1171.21,-695.328 1152,-642.21 1152,-595 1152,-595 1152,-595 1152,-521 1152,-480.553 1154.94,-465.98 1133,-432 1125.28,-420.038 1113.84,-409.843 1102.35,-401.685"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1104.28,-398.765 1094.02,-396.109 1100.39,-404.581 1104.28,-398.765"/>
</g>
-<!-- 21->10 -->
-<g id="edge28" class="edge"><title>21->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1289.78,-431.963C1273.11,-423.835 1256.58,-412.231 1247,-396 1238.87,-382.221 1238.87,-373.779 1247,-360 1259.61,-338.628 1284.27,-325.279 1305.44,-317.324"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1306.88,-320.53 1315.17,-313.94 1304.58,-313.918 1306.88,-320.53"/>
+<!-- 26 -->
+<g id="node27" class="node"><title>26</title>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M1753.5,-684C1753.5,-684 1680.5,-684 1680.5,-684 1674.5,-684 1668.5,-678 1668.5,-672 1668.5,-672 1668.5,-660 1668.5,-660 1668.5,-654 1674.5,-648 1680.5,-648 1680.5,-648 1753.5,-648 1753.5,-648 1759.5,-648 1765.5,-654 1765.5,-660 1765.5,-660 1765.5,-672 1765.5,-672 1765.5,-678 1759.5,-684 1753.5,-684"/>
+<text text-anchor="middle" x="1717" y="-663.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
-<!-- 22 -->
-<g id="node23" class="node"><title>22</title>
-<path fill="none" stroke="#d88d56" stroke-width="2" d="M1418,-396C1418,-396 1268,-396 1268,-396 1262,-396 1256,-390 1256,-384 1256,-384 1256,-372 1256,-372 1256,-366 1262,-360 1268,-360 1268,-360 1418,-360 1418,-360 1424,-360 1430,-366 1430,-372 1430,-372 1430,-384 1430,-384 1430,-390 1424,-396 1418,-396"/>
-<text text-anchor="middle" x="1343" y="-381" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
-<text text-anchor="middle" x="1343" y="-370" font-family="sans" font-size="10.00">seqmode: paired_end</text>
+<!-- 20->26 -->
+<g id="edge54" class="edge"><title>20->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1250.2,-731.219C1352.16,-717.192 1557.56,-688.934 1658.42,-675.059"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1659,-678.512 1668.43,-673.682 1658.05,-671.577 1659,-678.512"/>
</g>
-<!-- 21->22 -->
-<g id="edge49" class="edge"><title>21->22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1343,-431.697C1343,-423.983 1343,-414.712 1343,-406.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1346.5,-406.104 1343,-396.104 1339.5,-406.104 1346.5,-406.104"/>
+<!-- 21 -->
+<g id="node22" class="node"><title>21</title>
+<path fill="none" stroke="#97d856" stroke-width="2" d="M1607,-468C1607,-468 1531,-468 1531,-468 1525,-468 1519,-462 1519,-456 1519,-456 1519,-444 1519,-444 1519,-438 1525,-432 1531,-432 1531,-432 1607,-432 1607,-432 1613,-432 1619,-438 1619,-444 1619,-444 1619,-456 1619,-456 1619,-462 1613,-468 1607,-468"/>
+<text text-anchor="middle" x="1569" y="-447.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
</g>
-<!-- 31 -->
-<g id="node32" class="node"><title>31</title>
-<path fill="none" stroke="#b6d856" stroke-width="2" d="M1520,-324C1520,-324 1432,-324 1432,-324 1426,-324 1420,-318 1420,-312 1420,-312 1420,-300 1420,-300 1420,-294 1426,-288 1432,-288 1432,-288 1520,-288 1520,-288 1526,-288 1532,-294 1532,-300 1532,-300 1532,-312 1532,-312 1532,-318 1526,-324 1520,-324"/>
-<text text-anchor="middle" x="1476" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<!-- 21->8 -->
+<g id="edge22" class="edge"><title>21->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1535,-431.876C1516.4,-422.512 1493.17,-410.814 1473.29,-400.803"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1474.64,-397.562 1464.13,-396.19 1471.49,-403.814 1474.64,-397.562"/>
</g>
-<!-- 21->31 -->
-<g id="edge56" class="edge"><title>21->31</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1387.92,-431.937C1405.7,-423.364 1425.16,-411.461 1439,-396 1454.73,-378.433 1464.35,-353.241 1469.82,-334.14"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1473.27,-334.805 1472.45,-324.242 1466.5,-333.01 1473.27,-334.805"/>
+<!-- 22->9 -->
+<g id="edge23" class="edge"><title>22->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M963.385,-359.876C985.395,-350.307 1013.01,-338.3 1036.36,-328.148"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1037.97,-331.265 1045.74,-324.068 1035.18,-324.846 1037.97,-331.265"/>
</g>
<!-- 22->10 -->
-<g id="edge29" class="edge"><title>22->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1343,-359.697C1343,-351.983 1343,-342.712 1343,-334.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1346.5,-334.104 1343,-324.104 1339.5,-334.104 1346.5,-334.104"/>
-</g>
-<!-- 22->31 -->
-<g id="edge57" class="edge"><title>22->31</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1375.54,-359.876C1393.25,-350.554 1415.35,-338.919 1434.32,-328.939"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1436.12,-331.944 1443.34,-324.19 1432.86,-325.75 1436.12,-331.944"/>
+<g id="edge25" class="edge"><title>22->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M987.686,-362.1C990.834,-361.385 993.952,-360.682 997,-360 1051.64,-347.776 1113.21,-334.563 1161.21,-324.387"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1162.19,-327.759 1171.24,-322.264 1160.74,-320.911 1162.19,-327.759"/>
+</g>
+<!-- 22->11 -->
+<g id="edge27" class="edge"><title>22->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M880.946,-359.876C856.671,-350.222 826.16,-338.087 800.492,-327.878"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="801.5,-324.512 790.915,-324.068 798.913,-331.016 801.5,-324.512"/>
+</g>
+<!-- 22->12 -->
+<g id="edge29" class="edge"><title>22->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M923.258,-359.697C922.928,-351.983 922.531,-342.712 922.162,-334.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="925.658,-333.945 921.733,-324.104 918.665,-334.245 925.658,-333.945"/>
+</g>
+<!-- 23->9 -->
+<g id="edge24" class="edge"><title>23->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1066.93,-359.697C1069.61,-351.898 1072.83,-342.509 1075.8,-333.829"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1079.2,-334.699 1079.14,-324.104 1072.58,-332.429 1079.2,-334.699"/>
+</g>
+<!-- 23->10 -->
+<g id="edge26" class="edge"><title>23->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1105.77,-359.876C1131.12,-350.179 1163.01,-337.98 1189.77,-327.743"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1191.29,-330.91 1199.38,-324.068 1188.79,-324.372 1191.29,-330.91"/>
</g>
<!-- 23->11 -->
-<g id="edge30" class="edge"><title>23->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1765.69,-446.525C1801.26,-441.86 1847.27,-429.261 1871,-396 1884.22,-377.466 1875.57,-351.952 1865.31,-332.991"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1868.29,-331.152 1860.23,-324.269 1862.24,-334.673 1868.29,-331.152"/>
+<g id="edge28" class="edge"><title>23->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1005.19,-362.001C1002.43,-361.312 999.684,-360.642 997,-360 943.625,-347.239 883.449,-334.389 835.625,-324.537"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="836.114,-321.065 825.615,-322.482 834.706,-327.922 836.114,-321.065"/>
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-<!-- 24 -->
-<g id="node25" class="node"><title>24</title>
-<path fill="none" stroke="#d88d56" stroke-width="2" d="M1850,-396C1850,-396 1700,-396 1700,-396 1694,-396 1688,-390 1688,-384 1688,-384 1688,-372 1688,-372 1688,-366 1694,-360 1700,-360 1700,-360 1850,-360 1850,-360 1856,-360 1862,-366 1862,-372 1862,-372 1862,-384 1862,-384 1862,-390 1856,-396 1850,-396"/>
-<text text-anchor="middle" x="1775" y="-381" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
-<text text-anchor="middle" x="1775" y="-370" font-family="sans" font-size="10.00">seqmode: single_end</text>
+<!-- 23->12 -->
+<g id="edge30" class="edge"><title>23->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1026.75,-359.876C1007.94,-350.469 984.415,-338.708 964.334,-328.667"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="965.889,-325.531 955.38,-324.19 962.759,-331.792 965.889,-325.531"/>
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-<!-- 23->24 -->
-<g id="edge52" class="edge"><title>23->24</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1731.34,-431.697C1738.29,-423.305 1746.77,-413.07 1754.4,-403.861"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1757.14,-406.038 1760.83,-396.104 1751.75,-401.571 1757.14,-406.038"/>
+<!-- 24->13 -->
+<g id="edge31" class="edge"><title>24->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1289.78,-647.963C1273.11,-639.835 1256.58,-628.231 1247,-612 1238.87,-598.221 1238.87,-589.779 1247,-576 1259.61,-554.628 1284.27,-541.279 1305.44,-533.324"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1306.88,-536.53 1315.17,-529.94 1304.58,-529.918 1306.88,-536.53"/>
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-<!-- 32 -->
-<g id="node33" class="node"><title>32</title>
-<path fill="none" stroke="#b6d856" stroke-width="2" d="M1668,-324C1668,-324 1580,-324 1580,-324 1574,-324 1568,-318 1568,-312 1568,-312 1568,-300 1568,-300 1568,-294 1574,-288 1580,-288 1580,-288 1668,-288 1668,-288 1674,-288 1680,-294 1680,-300 1680,-300 1680,-312 1680,-312 1680,-318 1674,-324 1668,-324"/>
-<text text-anchor="middle" x="1624" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<!-- 25 -->
+<g id="node26" class="node"><title>25</title>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M1418,-612C1418,-612 1268,-612 1268,-612 1262,-612 1256,-606 1256,-600 1256,-600 1256,-588 1256,-588 1256,-582 1262,-576 1268,-576 1268,-576 1418,-576 1418,-576 1424,-576 1430,-582 1430,-588 1430,-588 1430,-600 1430,-600 1430,-606 1424,-612 1418,-612"/>
+<text text-anchor="middle" x="1343" y="-597" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="1343" y="-586" font-family="sans" font-size="10.00">seqmode: paired_end</text>
</g>
-<!-- 23->32 -->
-<g id="edge59" class="edge"><title>23->32</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1704.03,-431.545C1696.54,-421.31 1687.04,-408.06 1679,-396 1665.11,-375.148 1650.21,-350.925 1639.44,-333.019"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1642.34,-331.061 1634.2,-324.282 1636.34,-334.659 1642.34,-331.061"/>
+<!-- 24->25 -->
+<g id="edge52" class="edge"><title>24->25</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1343,-647.697C1343,-639.983 1343,-630.712 1343,-622.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1346.5,-622.104 1343,-612.104 1339.5,-622.104 1346.5,-622.104"/>
</g>
-<!-- 24->11 -->
-<g id="edge31" class="edge"><title>24->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1793.04,-359.697C1802.06,-351.05 1813.12,-340.449 1822.94,-331.027"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1825.37,-333.552 1830.16,-324.104 1820.52,-328.499 1825.37,-333.552"/>
+<!-- 34 -->
+<g id="node35" class="node"><title>34</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M1520,-540C1520,-540 1432,-540 1432,-540 1426,-540 1420,-534 1420,-528 1420,-528 1420,-516 1420,-516 1420,-510 1426,-504 1432,-504 1432,-504 1520,-504 1520,-504 1526,-504 1532,-510 1532,-516 1532,-516 1532,-528 1532,-528 1532,-534 1526,-540 1520,-540"/>
+<text text-anchor="middle" x="1476" y="-519.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
-<!-- 24->32 -->
-<g id="edge60" class="edge"><title>24->32</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1738.06,-359.876C1717.51,-350.349 1691.75,-338.407 1669.91,-328.283"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1671.36,-325.099 1660.82,-324.068 1668.42,-331.45 1671.36,-325.099"/>
+<!-- 24->34 -->
+<g id="edge59" class="edge"><title>24->34</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1387.92,-647.937C1405.7,-639.364 1425.16,-627.461 1439,-612 1454.73,-594.433 1464.35,-569.241 1469.82,-550.14"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1473.27,-550.805 1472.45,-540.242 1466.5,-549.01 1473.27,-550.805"/>
</g>
-<!-- 25->12 -->
-<g id="edge32" class="edge"><title>25->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1459.97,-215.876C1472.55,-206.893 1488.13,-195.763 1501.75,-186.034"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1503.83,-188.85 1509.93,-180.19 1499.76,-183.154 1503.83,-188.85"/>
+<!-- 25->13 -->
+<g id="edge32" class="edge"><title>25->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1343,-575.697C1343,-567.983 1343,-558.712 1343,-550.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1346.5,-550.104 1343,-540.104 1339.5,-550.104 1346.5,-550.104"/>
</g>
-<!-- 26 -->
-<g id="node27" class="node"><title>26</title>
-<path fill="none" stroke="#97d856" stroke-width="2" d="M1729,-252C1729,-252 1649,-252 1649,-252 1643,-252 1637,-246 1637,-240 1637,-240 1637,-228 1637,-228 1637,-222 1643,-216 1649,-216 1649,-216 1729,-216 1729,-216 1735,-216 1741,-222 1741,-228 1741,-228 1741,-240 1741,-240 1741,-246 1735,-252 1729,-252"/>
-<text text-anchor="middle" x="1689" y="-231.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
+<!-- 25->34 -->
+<g id="edge60" class="edge"><title>25->34</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1375.54,-575.876C1393.25,-566.554 1415.35,-554.919 1434.32,-544.939"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1436.12,-547.944 1443.34,-540.19 1432.86,-541.75 1436.12,-547.944"/>
</g>
-<!-- 26->12 -->
-<g id="edge33" class="edge"><title>26->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1651.08,-215.876C1626.56,-204.799 1594.8,-190.457 1570.55,-179.504"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1571.87,-176.264 1561.32,-175.338 1568.99,-182.643 1571.87,-176.264"/>
+<!-- 26->14 -->
+<g id="edge33" class="edge"><title>26->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1765.69,-662.525C1801.26,-657.86 1847.27,-645.261 1871,-612 1884.22,-593.466 1875.57,-567.952 1865.31,-548.991"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1868.29,-547.152 1860.23,-540.269 1862.24,-550.673 1868.29,-547.152"/>
</g>
-<!-- 26->13 -->
-<g id="edge35" class="edge"><title>26->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1684.06,-215.697C1681.83,-207.898 1679.15,-198.509 1676.67,-189.829"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1680,-188.758 1673.89,-180.104 1673.27,-190.681 1680,-188.758"/>
+<!-- 27 -->
+<g id="node28" class="node"><title>27</title>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M1850,-612C1850,-612 1700,-612 1700,-612 1694,-612 1688,-606 1688,-600 1688,-600 1688,-588 1688,-588 1688,-582 1694,-576 1700,-576 1700,-576 1850,-576 1850,-576 1856,-576 1862,-582 1862,-588 1862,-588 1862,-600 1862,-600 1862,-606 1856,-612 1850,-612"/>
+<text text-anchor="middle" x="1775" y="-597" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="1775" y="-586" font-family="sans" font-size="10.00">seqmode: single_end</text>
</g>
-<!-- 27->13 -->
-<g id="edge34" class="edge"><title>27->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1786.08,-215.876C1761.56,-204.799 1729.8,-190.457 1705.55,-179.504"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1706.87,-176.264 1696.32,-175.338 1703.99,-182.643 1706.87,-176.264"/>
+<!-- 26->27 -->
+<g id="edge55" class="edge"><title>26->27</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1731.34,-647.697C1738.29,-639.305 1746.77,-629.07 1754.4,-619.861"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1757.14,-622.038 1760.83,-612.104 1751.75,-617.571 1757.14,-622.038"/>
</g>
-<!-- 28 -->
-<g id="node29" class="node"><title>28</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M994,-617C994,-617 726,-617 726,-617 720,-617 714,-611 714,-605 714,-605 714,-593 714,-593 714,-587 720,-581 726,-581 726,-581 994,-581 994,-581 1000,-581 1006,-587 1006,-593 1006,-593 1006,-605 1006,-605 1006,-611 1000,-617 994,-617"/>
-<text text-anchor="middle" x="860" y="-602" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="860" y="-591" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+<!-- 35 -->
+<g id="node36" class="node"><title>35</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M1668,-540C1668,-540 1580,-540 1580,-540 1574,-540 1568,-534 1568,-528 1568,-528 1568,-516 1568,-516 1568,-510 1574,-504 1580,-504 1580,-504 1668,-504 1668,-504 1674,-504 1680,-510 1680,-516 1680,-516 1680,-528 1680,-528 1680,-534 1674,-540 1668,-540"/>
+<text text-anchor="middle" x="1624" y="-519.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+</g>
+<!-- 26->35 -->
+<g id="edge62" class="edge"><title>26->35</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1704.03,-647.545C1696.54,-637.31 1687.04,-624.06 1679,-612 1665.11,-591.148 1650.21,-566.925 1639.44,-549.019"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1642.34,-547.061 1634.2,-540.282 1636.34,-550.659 1642.34,-547.061"/>
+</g>
+<!-- 27->14 -->
+<g id="edge34" class="edge"><title>27->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1793.04,-575.697C1802.06,-567.05 1813.12,-556.449 1822.94,-547.027"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1825.37,-549.552 1830.16,-540.104 1820.52,-544.499 1825.37,-549.552"/>
+</g>
+<!-- 27->35 -->
+<g id="edge63" class="edge"><title>27->35</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1738.06,-575.876C1717.51,-566.349 1691.75,-554.407 1669.91,-544.283"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1671.36,-541.099 1660.82,-540.068 1668.42,-547.45 1671.36,-541.099"/>
</g>
<!-- 28->15 -->
-<g id="edge38" class="edge"><title>28->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M860,-580.819C860,-572.422 860,-562.116 860,-552.686"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="863.5,-552.558 860,-542.558 856.5,-552.558 863.5,-552.558"/>
+<g id="edge35" class="edge"><title>28->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1459.97,-431.876C1472.55,-422.893 1488.13,-411.763 1501.75,-402.034"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1503.83,-404.85 1509.93,-396.19 1499.76,-399.154 1503.83,-404.85"/>
</g>
<!-- 29 -->
<g id="node30" class="node"><title>29</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M1056.5,-324C1056.5,-324 955.5,-324 955.5,-324 949.5,-324 943.5,-318 943.5,-312 943.5,-312 943.5,-300 943.5,-300 943.5,-294 949.5,-288 955.5,-288 955.5,-288 1056.5,-288 1056.5,-288 1062.5,-288 1068.5,-294 1068.5,-300 1068.5,-300 1068.5,-312 1068.5,-312 1068.5,-318 1062.5,-324 1056.5,-324"/>
-<text text-anchor="middle" x="1006" y="-309" font-family="sans" font-size="10.00">extract_transcriptome</text>
-<text text-anchor="middle" x="1006" y="-298" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+<path fill="none" stroke="#a7d856" stroke-width="2" d="M1729,-468C1729,-468 1649,-468 1649,-468 1643,-468 1637,-462 1637,-456 1637,-456 1637,-444 1637,-444 1637,-438 1643,-432 1649,-432 1649,-432 1729,-432 1729,-432 1735,-432 1741,-438 1741,-444 1741,-444 1741,-456 1741,-456 1741,-462 1735,-468 1729,-468"/>
+<text text-anchor="middle" x="1689" y="-447.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
</g>
-<!-- 29->16 -->
-<g id="edge39" class="edge"><title>29->16</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1021.82,-287.697C1029.57,-279.22 1039.04,-268.864 1047.52,-259.583"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1050.2,-261.846 1054.36,-252.104 1045.03,-257.123 1050.2,-261.846"/>
+<!-- 29->15 -->
+<g id="edge36" class="edge"><title>29->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1651.08,-431.876C1626.56,-420.799 1594.8,-406.457 1570.55,-395.504"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1571.87,-392.264 1561.32,-391.338 1568.99,-398.643 1571.87,-392.264"/>
</g>
-<!-- 33 -->
-<g id="node34" class="node"><title>33</title>
-<path fill="none" stroke="#56d892" stroke-width="2" d="M985.5,-252C985.5,-252 900.5,-252 900.5,-252 894.5,-252 888.5,-246 888.5,-240 888.5,-240 888.5,-228 888.5,-228 888.5,-222 894.5,-216 900.5,-216 900.5,-216 985.5,-216 985.5,-216 991.5,-216 997.5,-222 997.5,-228 997.5,-228 997.5,-240 997.5,-240 997.5,-246 991.5,-252 985.5,-252"/>
-<text text-anchor="middle" x="943" y="-237" font-family="sans" font-size="10.00">create_index_salmon</text>
-<text text-anchor="middle" x="943" y="-226" font-family="sans" font-size="10.00">kmer: 31</text>
-</g>
-<!-- 29->33 -->
-<g id="edge62" class="edge"><title>29->33</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M990.427,-287.697C982.798,-279.22 973.477,-268.864 965.124,-259.583"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="967.685,-257.196 958.394,-252.104 962.482,-261.879 967.685,-257.196"/>
+<!-- 29->16 -->
+<g id="edge38" class="edge"><title>29->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1684.06,-431.697C1681.83,-423.898 1679.15,-414.509 1676.67,-405.829"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1680,-404.758 1673.89,-396.104 1673.27,-406.681 1680,-404.758"/>
</g>
-<!-- 30 -->
-<g id="node31" class="node"><title>30</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M1330,-617C1330,-617 1050,-617 1050,-617 1044,-617 1038,-611 1038,-605 1038,-605 1038,-593 1038,-593 1038,-587 1044,-581 1050,-581 1050,-581 1330,-581 1330,-581 1336,-581 1342,-587 1342,-593 1342,-593 1342,-605 1342,-605 1342,-611 1336,-617 1330,-617"/>
-<text text-anchor="middle" x="1190" y="-602" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1190" y="-591" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+<!-- 30->16 -->
+<g id="edge37" class="edge"><title>30->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1786.08,-431.876C1761.56,-420.799 1729.8,-406.457 1705.55,-395.504"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1706.87,-392.264 1696.32,-391.338 1703.99,-398.643 1706.87,-392.264"/>
</g>
-<!-- 30->17 -->
-<g id="edge40" class="edge"><title>30->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1190,-580.819C1190,-572.422 1190,-562.116 1190,-552.686"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1193.5,-552.558 1190,-542.558 1186.5,-552.558 1193.5,-552.558"/>
+<!-- 31 -->
+<g id="node32" class="node"><title>31</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M994,-833C994,-833 726,-833 726,-833 720,-833 714,-827 714,-821 714,-821 714,-809 714,-809 714,-803 720,-797 726,-797 726,-797 994,-797 994,-797 1000,-797 1006,-803 1006,-809 1006,-809 1006,-821 1006,-821 1006,-827 1000,-833 994,-833"/>
+<text text-anchor="middle" x="860" y="-818" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="860" y="-807" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g>
<!-- 31->18 -->
<g id="edge41" class="edge"><title>31->18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1498.99,-287.697C1510.81,-278.796 1525.39,-267.823 1538.18,-258.199"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1540.39,-260.915 1546.28,-252.104 1536.18,-255.322 1540.39,-260.915"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M860,-796.819C860,-788.422 860,-778.116 860,-768.686"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="863.5,-768.558 860,-758.558 856.5,-768.558 863.5,-768.558"/>
</g>
-<!-- 32->18 -->
-<g id="edge42" class="edge"><title>32->18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1610.4,-287.697C1603.88,-279.389 1595.93,-269.277 1588.75,-260.141"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1591.37,-257.805 1582.44,-252.104 1585.87,-262.13 1591.37,-257.805"/>
+<!-- 32 -->
+<g id="node33" class="node"><title>32</title>
+<path fill="none" stroke="#78d856" stroke-width="2" d="M1056.5,-540C1056.5,-540 955.5,-540 955.5,-540 949.5,-540 943.5,-534 943.5,-528 943.5,-528 943.5,-516 943.5,-516 943.5,-510 949.5,-504 955.5,-504 955.5,-504 1056.5,-504 1056.5,-504 1062.5,-504 1068.5,-510 1068.5,-516 1068.5,-516 1068.5,-528 1068.5,-528 1068.5,-534 1062.5,-540 1056.5,-540"/>
+<text text-anchor="middle" x="1006" y="-525" font-family="sans" font-size="10.00">extract_transcriptome</text>
+<text text-anchor="middle" x="1006" y="-514" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+</g>
+<!-- 32->19 -->
+<g id="edge42" class="edge"><title>32->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1021.82,-503.697C1029.57,-495.22 1039.04,-484.864 1047.52,-475.583"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1050.2,-477.846 1054.36,-468.104 1045.03,-473.123 1050.2,-477.846"/>
+</g>
+<!-- 36 -->
+<g id="node37" class="node"><title>36</title>
+<path fill="none" stroke="#59d856" stroke-width="2" d="M985.5,-468C985.5,-468 900.5,-468 900.5,-468 894.5,-468 888.5,-462 888.5,-456 888.5,-456 888.5,-444 888.5,-444 888.5,-438 894.5,-432 900.5,-432 900.5,-432 985.5,-432 985.5,-432 991.5,-432 997.5,-438 997.5,-444 997.5,-444 997.5,-456 997.5,-456 997.5,-462 991.5,-468 985.5,-468"/>
+<text text-anchor="middle" x="943" y="-453" font-family="sans" font-size="10.00">create_index_salmon</text>
+<text text-anchor="middle" x="943" y="-442" font-family="sans" font-size="10.00">kmer: 31</text>
+</g>
+<!-- 32->36 -->
+<g id="edge65" class="edge"><title>32->36</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M990.427,-503.697C982.798,-495.22 973.477,-484.864 965.124,-475.583"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="967.685,-473.196 958.394,-468.104 962.482,-477.879 967.685,-473.196"/>
</g>
-<!-- 33->19 -->
-<g id="edge44" class="edge"><title>33->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M938.303,-215.697C936.187,-207.898 933.638,-198.509 931.282,-189.829"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="934.64,-188.838 928.643,-180.104 927.884,-190.672 934.64,-188.838"/>
+<!-- 33 -->
+<g id="node34" class="node"><title>33</title>
+<path fill="none" stroke="#56b9d8" stroke-width="2" d="M1330,-833C1330,-833 1050,-833 1050,-833 1044,-833 1038,-827 1038,-821 1038,-821 1038,-809 1038,-809 1038,-803 1044,-797 1050,-797 1050,-797 1330,-797 1330,-797 1336,-797 1342,-803 1342,-809 1342,-809 1342,-821 1342,-821 1342,-827 1336,-833 1330,-833"/>
+<text text-anchor="middle" x="1190" y="-818" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="1190" y="-807" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
</g>
<!-- 33->20 -->
-<g id="edge46" class="edge"><title>33->20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M971.866,-215.876C987.295,-206.724 1006.48,-195.342 1023.1,-185.485"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1025.21,-188.302 1032.02,-180.19 1021.64,-182.282 1025.21,-188.302"/>
-</g>
-<!-- 34 -->
-<g id="node35" class="node"><title>34</title>
-<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1767.5,-545C1767.5,-545 1666.5,-545 1666.5,-545 1660.5,-545 1654.5,-539 1654.5,-533 1654.5,-533 1654.5,-516 1654.5,-516 1654.5,-510 1660.5,-504 1666.5,-504 1666.5,-504 1767.5,-504 1767.5,-504 1773.5,-504 1779.5,-510 1779.5,-516 1779.5,-516 1779.5,-533 1779.5,-533 1779.5,-539 1773.5,-545 1767.5,-545"/>
-<text text-anchor="middle" x="1717" y="-533" font-family="sans" font-size="10.00">create_index_star</text>
-<text text-anchor="middle" x="1717" y="-522" font-family="sans" font-size="10.00">index_size: 75</text>
-<text text-anchor="middle" x="1717" y="-511" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+<g id="edge43" class="edge"><title>33->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1190,-796.819C1190,-788.422 1190,-778.116 1190,-768.686"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1193.5,-768.558 1190,-758.558 1186.5,-768.558 1193.5,-768.558"/>
</g>
<!-- 34->21 -->
-<g id="edge47" class="edge"><title>34->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1654.4,-511.365C1586.62,-498.225 1478.92,-477.349 1409.61,-463.913"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1410.16,-460.453 1399.67,-461.986 1408.82,-467.325 1410.16,-460.453"/>
-</g>
-<!-- 34->23 -->
-<g id="edge50" class="edge"><title>34->23</title>
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+<polygon fill="grey" stroke="grey" stroke-width="2" points="1540.39,-476.915 1546.28,-468.104 1536.18,-471.322 1540.39,-476.915"/>
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+<polygon fill="grey" stroke="grey" stroke-width="2" points="1591.37,-473.805 1582.44,-468.104 1585.87,-478.13 1591.37,-473.805"/>
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+<polygon fill="grey" stroke="grey" stroke-width="2" points="934.64,-404.838 928.643,-396.104 927.884,-406.672 934.64,-404.838"/>
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+<path fill="none" stroke="grey" stroke-width="2" d="M971.866,-431.876C987.295,-422.724 1006.48,-411.342 1023.1,-401.485"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1025.21,-404.302 1032.02,-396.19 1021.64,-398.282 1025.21,-404.302"/>
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+<text text-anchor="middle" x="1717" y="-727" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
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+<!-- 37->24 -->
+<g id="edge50" class="edge"><title>37->24</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1654.4,-727.365C1586.62,-714.225 1478.92,-693.349 1409.61,-679.913"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1410.16,-676.453 1399.67,-677.986 1408.82,-683.325 1410.16,-676.453"/>
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+<!-- 37->26 -->
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+<polygon fill="grey" stroke="grey" stroke-width="2" points="1720.5,-694.319 1717,-684.319 1713.5,-694.32 1720.5,-694.319"/>
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+<path fill="none" stroke="grey" stroke-width="2" d="M1763.03,-719.97C1804.26,-699.684 1862.09,-663.634 1888,-612 1896.33,-595.398 1897.01,-518.975 1885,-504 1848.05,-457.922 1813.46,-481.709 1751.06,-468.017"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1751.78,-464.589 1741.23,-465.598 1750.11,-471.386 1751.78,-464.589"/>
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+<text text-anchor="middle" x="1559" y="-591.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+</g>
+<!-- 38->34 -->
+<g id="edge61" class="edge"><title>38->34</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1538.48,-575.697C1528.13,-566.965 1515.41,-556.24 1504.16,-546.75"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1506.18,-543.876 1496.28,-540.104 1501.67,-549.227 1506.18,-543.876"/>
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+<!-- 38->35 -->
+<g id="edge64" class="edge"><title>38->35</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1575.07,-575.697C1582.94,-567.22 1592.56,-556.864 1601.17,-547.583"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1603.88,-549.814 1608.12,-540.104 1598.75,-545.051 1603.88,-549.814"/>
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diff --git a/images/logo.128px.png b/images/logo.128px.png
new file mode 100644
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Binary files /dev/null and b/images/logo.128px.png differ
diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index ef56730d2ad5048d97675c173e2a3ed530ee1447..8de684c8bf4c85e35cda7d0e03faa8d2fb957ff8 100644
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<title>snakemake_dag</title>
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<path fill="none" stroke="#d85656" stroke-width="2" d="M339,-36C339,-36 309,-36 309,-36 303,-36 297,-30 297,-24 297,-24 297,-12 297,-12 297,-6 303,-0 309,-0 309,-0 339,-0 339,-0 345,-0 351,-6 351,-12 351,-12 351,-24 351,-24 351,-30 345,-36 339,-36"/>
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+<text text-anchor="middle" x="324" y="-87.5" font-family="sans" font-size="10.00">MULTIQC_report</text>
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-<text text-anchor="middle" x="114" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
+<path fill="none" stroke="#c6d856" stroke-width="2" d="M373,-180C373,-180 275,-180 275,-180 269,-180 263,-174 263,-168 263,-168 263,-156 263,-156 263,-150 269,-144 275,-144 275,-144 373,-144 373,-144 379,-144 385,-150 385,-156 385,-156 385,-168 385,-168 385,-174 379,-180 373,-180"/>
+<text text-anchor="middle" x="324" y="-159.5" font-family="sans" font-size="10.00">prepare_MultiQC_config</text>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="288.199,-32.865 296.823,-26.7106 286.244,-26.1437 288.199,-32.865"/>
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+<polygon fill="grey" stroke="grey" stroke-width="2" points="327.5,-118.104 324,-108.104 320.5,-118.104 327.5,-118.104"/>
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<g id="node4" class="node"><title>3</title>
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-<text text-anchor="middle" x="83" y="-447.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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+<text text-anchor="middle" x="324" y="-231.5" font-family="sans" font-size="10.00">prepare_files_for_report</text>
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+<path fill="none" stroke="grey" stroke-width="2" d="M324,-215.697C324,-207.983 324,-198.712 324,-190.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="327.5,-190.104 324,-180.104 320.5,-190.104 327.5,-190.104"/>
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-<text text-anchor="middle" x="259" y="-447.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
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+<text text-anchor="middle" x="39" y="-303.5" font-family="sans" font-size="10.00">pe_fastqc</text>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="290.649,-44.0444 296.864,-35.4639 286.654,-38.2958 290.649,-44.0444"/>
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<g id="node6" class="node"><title>5</title>
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-<text text-anchor="middle" x="478" y="-159.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
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+<text text-anchor="middle" x="114" y="-303.5" font-family="sans" font-size="10.00">fastqc</text>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="352.366,-40.395 342.642,-36.1893 347.621,-45.5412 352.366,-40.395"/>
+<!-- 5->3 -->
+<g id="edge13" class="edge"><title>5->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M141.214,-293.319C145.789,-291.47 150.51,-289.631 155,-288 187.729,-276.11 224.572,-264.368 255.485,-254.97"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="256.741,-258.247 265.301,-252.003 254.716,-251.546 256.741,-258.247"/>
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<g id="node7" class="node"><title>6</title>
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-<text text-anchor="middle" x="303" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
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+<text text-anchor="middle" x="83" y="-663.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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-<text text-anchor="middle" x="467" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
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+<g id="edge5" class="edge"><title>7->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M246.068,-647.677C239.186,-637.702 231.112,-624.665 226,-612 210.862,-574.493 207,-563.447 207,-523 207,-523 207,-523 207,-377 207,-325.614 253.2,-282.737 287.537,-257.966"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="289.787,-260.664 295.976,-252.064 285.775,-254.927 289.787,-260.664"/>
</g>
<!-- 8 -->
<g id="node9" class="node"><title>8</title>
-<path fill="none" stroke="#566bd8" stroke-width="2" d="M866.5,-324C866.5,-324 835.5,-324 835.5,-324 829.5,-324 823.5,-318 823.5,-312 823.5,-312 823.5,-300 823.5,-300 823.5,-294 829.5,-288 835.5,-288 835.5,-288 866.5,-288 866.5,-288 872.5,-288 878.5,-294 878.5,-300 878.5,-300 878.5,-312 878.5,-312 878.5,-318 872.5,-324 866.5,-324"/>
-<text text-anchor="middle" x="851" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
+<path fill="none" stroke="#68d856" stroke-width="2" d="M510.5,-396C510.5,-396 445.5,-396 445.5,-396 439.5,-396 433.5,-390 433.5,-384 433.5,-384 433.5,-372 433.5,-372 433.5,-366 439.5,-360 445.5,-360 445.5,-360 510.5,-360 510.5,-360 516.5,-360 522.5,-366 522.5,-372 522.5,-372 522.5,-384 522.5,-384 522.5,-390 516.5,-396 510.5,-396"/>
+<text text-anchor="middle" x="478" y="-375.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
</g>
-<!-- 8->0 -->
-<g id="edge10" class="edge"><title>8->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M823.408,-290.026C735.084,-242.093 459.299,-92.4259 360.045,-38.5615"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="361.462,-35.3482 351.003,-33.6545 358.123,-41.5006 361.462,-35.3482"/>
-</g>
-<!-- 20 -->
-<g id="node21" class="node"><title>20</title>
-<path fill="none" stroke="#56d873" stroke-width="2" d="M903,-252C903,-252 797,-252 797,-252 791,-252 785,-246 785,-240 785,-240 785,-228 785,-228 785,-222 791,-216 797,-216 797,-216 903,-216 903,-216 909,-216 915,-222 915,-228 915,-228 915,-240 915,-240 915,-246 909,-252 903,-252"/>
-<text text-anchor="middle" x="850" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
-</g>
-<!-- 8->20 -->
-<g id="edge40" class="edge"><title>8->20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M850.753,-287.697C850.643,-279.983 850.51,-270.712 850.387,-262.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="853.887,-262.053 850.244,-252.104 846.888,-262.153 853.887,-262.053"/>
+<!-- 8->3 -->
+<g id="edge8" class="edge"><title>8->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M459.424,-359.871C432.137,-334.711 381.103,-287.654 350.073,-259.042"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="352.366,-256.395 342.642,-252.189 347.621,-261.541 352.366,-256.395"/>
</g>
<!-- 9 -->
<g id="node10" class="node"><title>9</title>
-<path fill="none" stroke="#d8ac56" stroke-width="2" d="M850,-180C850,-180 820,-180 820,-180 814,-180 808,-174 808,-168 808,-168 808,-156 808,-156 808,-150 814,-144 820,-144 820,-144 850,-144 850,-144 856,-144 862,-150 862,-156 862,-156 862,-168 862,-168 862,-174 856,-180 850,-180"/>
-<text text-anchor="middle" x="835" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
+<path fill="none" stroke="#569ad8" stroke-width="2" d="M359,-612C359,-612 247,-612 247,-612 241,-612 235,-606 235,-600 235,-600 235,-588 235,-588 235,-582 241,-576 247,-576 247,-576 359,-576 359,-576 365,-576 371,-582 371,-588 371,-588 371,-600 371,-600 371,-606 365,-612 359,-612"/>
+<text text-anchor="middle" x="303" y="-591.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
</g>
-<!-- 9->0 -->
-<g id="edge5" class="edge"><title>9->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M807.667,-145.655C789.461,-135.295 765.097,-121.159 744,-108 719.526,-92.7346 716.935,-82.3204 690,-72 575.896,-28.28 429.165,-20.273 361.382,-19.0424"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="361.247,-15.5402 351.199,-18.8986 361.148,-22.5395 361.247,-15.5402"/>
+<!-- 9->3 -->
+<g id="edge9" class="edge"><title>9->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M303.198,-575.951C303.489,-549.292 304,-496.116 304,-451 304,-451 304,-451 304,-377 304,-336.822 311.948,-290.869 317.823,-262.389"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="321.296,-262.887 319.953,-252.378 314.449,-261.431 321.296,-262.887"/>
</g>
<!-- 10 -->
<g id="node11" class="node"><title>10</title>
-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M846.5,-108C846.5,-108 765.5,-108 765.5,-108 759.5,-108 753.5,-102 753.5,-96 753.5,-96 753.5,-84 753.5,-84 753.5,-78 759.5,-72 765.5,-72 765.5,-72 846.5,-72 846.5,-72 852.5,-72 858.5,-78 858.5,-84 858.5,-84 858.5,-96 858.5,-96 858.5,-102 852.5,-108 846.5,-108"/>
-<text text-anchor="middle" x="806" y="-87.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
-</g>
-<!-- 9->10 -->
-<g id="edge25" class="edge"><title>9->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M827.831,-143.697C824.565,-135.813 820.626,-126.304 816.998,-117.546"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="820.147,-116.003 813.086,-108.104 813.68,-118.683 820.147,-116.003"/>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M532.5,-612C532.5,-612 401.5,-612 401.5,-612 395.5,-612 389.5,-606 389.5,-600 389.5,-600 389.5,-588 389.5,-588 389.5,-582 395.5,-576 401.5,-576 401.5,-576 532.5,-576 532.5,-576 538.5,-576 544.5,-582 544.5,-588 544.5,-588 544.5,-600 544.5,-600 544.5,-606 538.5,-612 532.5,-612"/>
+<text text-anchor="middle" x="467" y="-591.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
</g>
-<!-- 10->0 -->
-<g id="edge2" class="edge"><title>10->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M753.403,-75.7453C747.22,-74.3834 740.984,-73.0989 735,-72 598.087,-46.8556 433.355,-29.4441 361.065,-22.4398"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="361.372,-18.9533 351.084,-21.4822 360.704,-25.9213 361.372,-18.9533"/>
+<!-- 10->3 -->
+<g id="edge4" class="edge"><title>10->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M436.911,-575.894C400.497,-552.696 344,-507.588 344,-451 344,-451 344,-451 344,-377 344,-336.822 336.052,-290.869 330.177,-262.389"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="333.551,-261.431 328.047,-252.378 326.704,-262.887 333.551,-261.431"/>
</g>
<!-- 11 -->
<g id="node12" class="node"><title>11</title>
-<path fill="none" stroke="#a7d856" stroke-width="2" d="M395,-540C395,-540 283,-540 283,-540 277,-540 271,-534 271,-528 271,-528 271,-516 271,-516 271,-510 277,-504 283,-504 283,-504 395,-504 395,-504 401,-504 407,-510 407,-516 407,-516 407,-528 407,-528 407,-534 401,-540 395,-540"/>
-<text text-anchor="middle" x="339" y="-519.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+<path fill="none" stroke="#d87556" stroke-width="2" d="M866.5,-540C866.5,-540 835.5,-540 835.5,-540 829.5,-540 823.5,-534 823.5,-528 823.5,-528 823.5,-516 823.5,-516 823.5,-510 829.5,-504 835.5,-504 835.5,-504 866.5,-504 866.5,-504 872.5,-504 878.5,-510 878.5,-516 878.5,-516 878.5,-528 878.5,-528 878.5,-534 872.5,-540 866.5,-540"/>
+<text text-anchor="middle" x="851" y="-519.5" font-family="sans" font-size="10.00">star_rpm</text>
</g>
<!-- 11->3 -->
<g id="edge11" class="edge"><title>11->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M276.703,-503.966C240.156,-493.972 193.806,-481.298 155.609,-470.854"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="156.146,-467.372 145.577,-468.111 154.299,-474.124 156.146,-467.372"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M823.408,-506.026C736.345,-458.777 467.135,-312.679 364.403,-256.927"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="366.024,-253.824 355.566,-252.131 362.686,-259.977 366.024,-253.824"/>
</g>
-<!-- 15 -->
-<g id="node16" class="node"><title>15</title>
-<path fill="none" stroke="#d89c56" stroke-width="2" d="M467.5,-468C467.5,-468 364.5,-468 364.5,-468 358.5,-468 352.5,-462 352.5,-456 352.5,-456 352.5,-444 352.5,-444 352.5,-438 358.5,-432 364.5,-432 364.5,-432 467.5,-432 467.5,-432 473.5,-432 479.5,-438 479.5,-444 479.5,-444 479.5,-456 479.5,-456 479.5,-462 473.5,-468 467.5,-468"/>
-<text text-anchor="middle" x="416" y="-447.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
-</g>
-<!-- 11->15 -->
-<g id="edge31" class="edge"><title>11->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M358.034,-503.697C367.545,-495.05 379.207,-484.449 389.57,-475.027"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="392.14,-477.421 397.185,-468.104 387.431,-472.241 392.14,-477.421"/>
-</g>
-<!-- 17 -->
-<g id="node18" class="node"><title>17</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M887.5,-468C887.5,-468 798.5,-468 798.5,-468 792.5,-468 786.5,-462 786.5,-456 786.5,-456 786.5,-444 786.5,-444 786.5,-438 792.5,-432 798.5,-432 798.5,-432 887.5,-432 887.5,-432 893.5,-432 899.5,-438 899.5,-444 899.5,-444 899.5,-456 899.5,-456 899.5,-462 893.5,-468 887.5,-468"/>
-<text text-anchor="middle" x="843" y="-447.5" 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="#56d88a" stroke-width="2" d="M903,-468C903,-468 797,-468 797,-468 791,-468 785,-462 785,-456 785,-456 785,-444 785,-444 785,-438 791,-432 797,-432 797,-432 903,-432 903,-432 909,-432 915,-438 915,-444 915,-444 915,-456 915,-456 915,-462 909,-468 903,-468"/>
+<text text-anchor="middle" x="850" y="-447.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
</g>
-<!-- 11->17 -->
-<g id="edge35" class="edge"><title>11->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M407.368,-505.557C410.28,-505.009 413.167,-504.487 416,-504 542.678,-482.204 691.979,-465.763 776.257,-457.326"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="776.852,-460.784 786.456,-456.312 776.159,-453.819 776.852,-460.784"/>
+<!-- 11->23 -->
+<g id="edge43" class="edge"><title>11->23</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M850.753,-503.697C850.643,-495.983 850.51,-486.712 850.387,-478.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="853.887,-478.053 850.244,-468.104 846.888,-478.153 853.887,-478.053"/>
</g>
<!-- 12 -->
<g id="node13" class="node"><title>12</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M237,-540C237,-540 153,-540 153,-540 147,-540 141,-534 141,-528 141,-528 141,-516 141,-516 141,-510 147,-504 153,-504 153,-504 237,-504 237,-504 243,-504 249,-510 249,-516 249,-516 249,-528 249,-528 249,-534 243,-540 237,-540"/>
-<text text-anchor="middle" x="195" y="-519.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M850,-396C850,-396 820,-396 820,-396 814,-396 808,-390 808,-384 808,-384 808,-372 808,-372 808,-366 814,-360 820,-360 820,-360 850,-360 850,-360 856,-360 862,-366 862,-372 862,-372 862,-384 862,-384 862,-390 856,-396 850,-396"/>
+<text text-anchor="middle" x="835" y="-375.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
<!-- 12->3 -->
<g id="edge12" class="edge"><title>12->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M167.602,-503.876C153.093,-494.808 135.084,-483.552 119.415,-473.759"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="120.839,-470.522 110.504,-468.19 117.129,-476.458 120.839,-470.522"/>
-</g>
-<!-- 12->4 -->
-<g id="edge14" class="edge"><title>12->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M210.82,-503.697C218.57,-495.22 228.039,-484.864 236.524,-475.583"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="239.197,-477.846 243.362,-468.104 234.031,-473.123 239.197,-477.846"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M807.667,-361.655C789.461,-351.295 765.097,-337.159 744,-324 719.526,-308.735 716.935,-298.32 690,-288 591.798,-250.373 469.428,-239.198 394.018,-236.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="393.823,-232.52 383.697,-235.634 393.555,-239.515 393.823,-232.52"/>
</g>
<!-- 13 -->
<g id="node14" class="node"><title>13</title>
-<path fill="none" stroke="#d8d356" stroke-width="2" d="M661,-540C661,-540 565,-540 565,-540 559,-540 553,-534 553,-528 553,-528 553,-516 553,-516 553,-510 559,-504 565,-504 565,-504 661,-504 661,-504 667,-504 673,-510 673,-516 673,-516 673,-528 673,-528 673,-534 667,-540 661,-540"/>
-<text text-anchor="middle" x="613" y="-519.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M846.5,-324C846.5,-324 765.5,-324 765.5,-324 759.5,-324 753.5,-318 753.5,-312 753.5,-312 753.5,-300 753.5,-300 753.5,-294 759.5,-288 765.5,-288 765.5,-288 846.5,-288 846.5,-288 852.5,-288 858.5,-294 858.5,-300 858.5,-300 858.5,-312 858.5,-312 858.5,-318 852.5,-324 846.5,-324"/>
+<text text-anchor="middle" x="806" y="-303.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
</g>
-<!-- 13->4 -->
-<g id="edge13" class="edge"><title>13->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M552.723,-506.118C549.439,-505.383 546.181,-504.672 543,-504 457.739,-485.99 433.404,-485.008 344.115,-468.184"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="344.567,-464.707 334.09,-466.28 343.261,-471.585 344.567,-464.707"/>
+<!-- 12->13 -->
+<g id="edge28" class="edge"><title>12->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M827.831,-359.697C824.565,-351.813 820.626,-342.304 816.998,-333.546"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="820.147,-332.003 813.086,-324.104 813.68,-334.683 820.147,-332.003"/>
</g>
-<!-- 16 -->
-<g id="node17" class="node"><title>16</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M596.5,-468C596.5,-468 509.5,-468 509.5,-468 503.5,-468 497.5,-462 497.5,-456 497.5,-456 497.5,-444 497.5,-444 497.5,-438 503.5,-432 509.5,-432 509.5,-432 596.5,-432 596.5,-432 602.5,-432 608.5,-438 608.5,-444 608.5,-444 608.5,-456 608.5,-456 608.5,-462 602.5,-468 596.5,-468"/>
-<text text-anchor="middle" x="553" y="-447.5" font-family="sans" font-size="10.00">quantification_salmon</text>
+<!-- 13->3 -->
+<g id="edge6" class="edge"><title>13->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M753.403,-291.745C747.22,-290.383 740.984,-289.099 735,-288 615.786,-266.106 475.48,-250.075 393.473,-241.672"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="393.825,-238.19 383.522,-240.661 393.117,-245.154 393.825,-238.19"/>
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-<!-- 13->16 -->
-<g id="edge33" class="edge"><title>13->16</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M598.169,-503.697C590.975,-495.305 582.203,-485.07 574.31,-475.861"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="576.826,-473.419 567.661,-468.104 571.511,-477.975 576.826,-473.419"/>
+<!-- 14 -->
+<g id="node15" class="node"><title>14</title>
+<path fill="none" stroke="#56d8d8" stroke-width="2" d="M395,-756C395,-756 283,-756 283,-756 277,-756 271,-750 271,-744 271,-744 271,-732 271,-732 271,-726 277,-720 283,-720 283,-720 395,-720 395,-720 401,-720 407,-726 407,-732 407,-732 407,-744 407,-744 407,-750 401,-756 395,-756"/>
+<text text-anchor="middle" x="339" y="-735.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
-<!-- 19 -->
-<g id="node20" class="node"><title>19</title>
-<path fill="none" stroke="#56d892" stroke-width="2" d="M1002.5,-468C1002.5,-468 929.5,-468 929.5,-468 923.5,-468 917.5,-462 917.5,-456 917.5,-456 917.5,-444 917.5,-444 917.5,-438 923.5,-432 929.5,-432 929.5,-432 1002.5,-432 1002.5,-432 1008.5,-432 1014.5,-438 1014.5,-444 1014.5,-444 1014.5,-456 1014.5,-456 1014.5,-462 1008.5,-468 1002.5,-468"/>
-<text text-anchor="middle" x="966" y="-447.5" font-family="sans" font-size="10.00">map_genome_star</text>
+<!-- 14->6 -->
+<g id="edge15" class="edge"><title>14->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M276.703,-719.966C240.156,-709.972 193.806,-697.298 155.609,-686.854"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="156.146,-683.372 145.577,-684.111 154.299,-690.124 156.146,-683.372"/>
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-<!-- 13->19 -->
-<g id="edge39" class="edge"><title>13->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M673.279,-512.113C731.011,-503.162 820.701,-488.115 907.607,-467.955"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="908.43,-471.357 917.367,-465.666 906.832,-464.542 908.43,-471.357"/>
+<!-- 18 -->
+<g id="node19" class="node"><title>18</title>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M467.5,-684C467.5,-684 364.5,-684 364.5,-684 358.5,-684 352.5,-678 352.5,-672 352.5,-672 352.5,-660 352.5,-660 352.5,-654 358.5,-648 364.5,-648 364.5,-648 467.5,-648 467.5,-648 473.5,-648 479.5,-654 479.5,-660 479.5,-660 479.5,-672 479.5,-672 479.5,-678 473.5,-684 467.5,-684"/>
+<text text-anchor="middle" x="416" y="-663.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
</g>
-<!-- 14 -->
-<g id="node15" class="node"><title>14</title>
-<path fill="none" stroke="#97d856" stroke-width="2" d="M577,-252C577,-252 501,-252 501,-252 495,-252 489,-246 489,-240 489,-240 489,-228 489,-228 489,-222 495,-216 501,-216 501,-216 577,-216 577,-216 583,-216 589,-222 589,-228 589,-228 589,-240 589,-240 589,-246 583,-252 577,-252"/>
-<text text-anchor="middle" x="539" y="-231.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
+<!-- 14->18 -->
+<g id="edge34" class="edge"><title>14->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M358.034,-719.697C367.545,-711.05 379.207,-700.449 389.57,-691.027"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="392.14,-693.421 397.185,-684.104 387.431,-688.241 392.14,-693.421"/>
+</g>
+<!-- 20 -->
+<g id="node21" class="node"><title>20</title>
+<path fill="none" stroke="#97d856" stroke-width="2" d="M887.5,-684C887.5,-684 798.5,-684 798.5,-684 792.5,-684 786.5,-678 786.5,-672 786.5,-672 786.5,-660 786.5,-660 786.5,-654 792.5,-648 798.5,-648 798.5,-648 887.5,-648 887.5,-648 893.5,-648 899.5,-654 899.5,-660 899.5,-660 899.5,-672 899.5,-672 899.5,-678 893.5,-684 887.5,-684"/>
+<text text-anchor="middle" x="843" y="-663.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+</g>
+<!-- 14->20 -->
+<g id="edge38" class="edge"><title>14->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M407.368,-721.557C410.28,-721.009 413.167,-720.487 416,-720 542.678,-698.204 691.979,-681.763 776.257,-673.326"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="776.852,-676.784 786.456,-672.312 776.159,-669.819 776.852,-676.784"/>
</g>
-<!-- 14->5 -->
-<g id="edge15" class="edge"><title>14->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M523.921,-215.697C516.608,-207.305 507.69,-197.07 499.665,-187.861"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="502.114,-185.344 492.905,-180.104 496.836,-189.943 502.114,-185.344"/>
+<!-- 15 -->
+<g id="node16" class="node"><title>15</title>
+<path fill="none" stroke="#56a9d8" stroke-width="2" d="M237,-756C237,-756 153,-756 153,-756 147,-756 141,-750 141,-744 141,-744 141,-732 141,-732 141,-726 147,-720 153,-720 153,-720 237,-720 237,-720 243,-720 249,-726 249,-732 249,-732 249,-744 249,-744 249,-750 243,-756 237,-756"/>
+<text text-anchor="middle" x="195" y="-735.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
</g>
<!-- 15->6 -->
-<g id="edge16" class="edge"><title>15->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M388.357,-431.876C373.582,-422.724 355.209,-411.342 339.297,-401.485"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="341.093,-398.481 330.749,-396.19 337.407,-404.431 341.093,-398.481"/>
+<g id="edge14" class="edge"><title>15->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M167.602,-719.876C153.093,-710.808 135.084,-699.552 119.415,-689.759"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="120.839,-686.522 110.504,-684.19 117.129,-692.458 120.839,-686.522"/>
</g>
<!-- 15->7 -->
-<g id="edge18" class="edge"><title>15->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M428.607,-431.697C434.597,-423.474 441.876,-413.483 448.479,-404.421"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="451.478,-406.248 454.538,-396.104 445.821,-402.126 451.478,-406.248"/>
+<g id="edge16" class="edge"><title>15->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M210.82,-719.697C218.57,-711.22 228.039,-700.864 236.524,-691.583"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="239.197,-693.846 243.362,-684.104 234.031,-689.123 239.197,-693.846"/>
</g>
-<!-- 16->6 -->
-<g id="edge17" class="edge"><title>16->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M497.206,-433.378C460.723,-423.163 412.756,-409.732 373.621,-398.774"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="374.447,-395.371 363.874,-396.045 372.56,-402.111 374.447,-395.371"/>
+<!-- 16 -->
+<g id="node17" class="node"><title>16</title>
+<path fill="none" stroke="#d89556" stroke-width="2" d="M661,-756C661,-756 565,-756 565,-756 559,-756 553,-750 553,-744 553,-744 553,-732 553,-732 553,-726 559,-720 565,-720 565,-720 661,-720 661,-720 667,-720 673,-726 673,-732 673,-732 673,-744 673,-744 673,-750 667,-756 661,-756"/>
+<text text-anchor="middle" x="613" y="-735.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
<!-- 16->7 -->
-<g id="edge19" class="edge"><title>16->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M531.742,-431.697C520.911,-422.881 507.582,-412.032 495.84,-402.474"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="497.979,-399.703 488.014,-396.104 493.56,-405.132 497.979,-399.703"/>
+<g id="edge17" class="edge"><title>16->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M552.723,-722.118C549.439,-721.383 546.181,-720.672 543,-720 457.739,-701.99 433.404,-701.008 344.115,-684.184"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="344.567,-680.707 334.09,-682.28 343.261,-687.585 344.567,-680.707"/>
</g>
-<!-- 17->8 -->
-<g id="edge20" class="edge"><title>17->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M899.722,-433.313C918.045,-425.265 936.359,-413.365 947,-396 955.359,-382.357 955.132,-373.779 947,-360 934.386,-338.628 909.727,-325.279 888.56,-317.324"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="889.422,-313.918 878.828,-313.94 887.123,-320.53 889.422,-313.918"/>
+<!-- 19 -->
+<g id="node20" class="node"><title>19</title>
+<path fill="none" stroke="#78d856" stroke-width="2" d="M596.5,-684C596.5,-684 509.5,-684 509.5,-684 503.5,-684 497.5,-678 497.5,-672 497.5,-672 497.5,-660 497.5,-660 497.5,-654 503.5,-648 509.5,-648 509.5,-648 596.5,-648 596.5,-648 602.5,-648 608.5,-654 608.5,-660 608.5,-660 608.5,-672 608.5,-672 608.5,-678 602.5,-684 596.5,-684"/>
+<text text-anchor="middle" x="553" y="-663.5" font-family="sans" font-size="10.00">quantification_salmon</text>
</g>
-<!-- 18 -->
-<g id="node19" class="node"><title>18</title>
-<path fill="none" stroke="#ced856" stroke-width="2" d="M926,-396C926,-396 776,-396 776,-396 770,-396 764,-390 764,-384 764,-384 764,-372 764,-372 764,-366 770,-360 776,-360 776,-360 926,-360 926,-360 932,-360 938,-366 938,-372 938,-372 938,-384 938,-384 938,-390 932,-396 926,-396"/>
-<text text-anchor="middle" x="851" y="-375.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<!-- 16->19 -->
+<g id="edge36" class="edge"><title>16->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M598.169,-719.697C590.975,-711.305 582.203,-701.07 574.31,-691.861"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="576.826,-689.419 567.661,-684.104 571.511,-693.975 576.826,-689.419"/>
</g>
-<!-- 17->18 -->
-<g id="edge36" class="edge"><title>17->18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M844.978,-431.697C845.859,-423.983 846.919,-414.712 847.901,-406.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="851.387,-406.437 849.045,-396.104 844.432,-405.642 851.387,-406.437"/>
+<!-- 22 -->
+<g id="node23" class="node"><title>22</title>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M1002.5,-684C1002.5,-684 929.5,-684 929.5,-684 923.5,-684 917.5,-678 917.5,-672 917.5,-672 917.5,-660 917.5,-660 917.5,-654 923.5,-648 929.5,-648 929.5,-648 1002.5,-648 1002.5,-648 1008.5,-648 1014.5,-654 1014.5,-660 1014.5,-660 1014.5,-672 1014.5,-672 1014.5,-678 1008.5,-684 1002.5,-684"/>
+<text text-anchor="middle" x="966" y="-663.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
-<!-- 25 -->
-<g id="node26" class="node"><title>25</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M780,-324C780,-324 692,-324 692,-324 686,-324 680,-318 680,-312 680,-312 680,-300 680,-300 680,-294 686,-288 692,-288 692,-288 780,-288 780,-288 786,-288 792,-294 792,-300 792,-300 792,-312 792,-312 792,-318 786,-324 780,-324"/>
-<text text-anchor="middle" x="736" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
-</g>
-<!-- 17->25 -->
-<g id="edge42" class="edge"><title>17->25</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M799.53,-431.827C783.272,-423.345 766.08,-411.537 755,-396 742.133,-377.959 737.662,-352.972 736.249,-334.065"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="739.741,-333.812 735.737,-324.002 732.75,-334.167 739.741,-333.812"/>
-</g>
-<!-- 18->8 -->
-<g id="edge21" class="edge"><title>18->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M851,-359.697C851,-351.983 851,-342.712 851,-334.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="854.5,-334.104 851,-324.104 847.5,-334.104 854.5,-334.104"/>
-</g>
-<!-- 18->25 -->
-<g id="edge44" class="edge"><title>18->25</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M822.868,-359.876C807.832,-350.724 789.133,-339.342 772.94,-329.485"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="774.602,-326.4 764.24,-324.19 770.962,-332.379 774.602,-326.4"/>
-</g>
-<!-- 19->8 -->
-<g id="edge22" class="edge"><title>19->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M970.876,-431.724C975.205,-412.573 978.916,-381.548 965,-360 948.17,-333.94 914.888,-320.48 888.609,-313.662"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="889.107,-310.183 878.57,-311.284 887.494,-316.994 889.107,-310.183"/>
-</g>
-<!-- 19->18 -->
-<g id="edge37" class="edge"><title>19->18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M937.868,-431.876C922.832,-422.724 904.133,-411.342 887.94,-401.485"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="889.602,-398.4 879.24,-396.19 885.962,-404.379 889.602,-398.4"/>
-</g>
-<!-- 19->25 -->
-<g id="edge45" class="edge"><title>19->25</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M967.332,-431.807C967.882,-411.847 965.54,-379.215 947,-360 941.799,-354.609 861.991,-335.541 802.055,-321.821"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="802.775,-318.395 792.247,-319.582 801.217,-325.22 802.775,-318.395"/>
-</g>
-<!-- 20->9 -->
-<g id="edge23" class="edge"><title>20->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M846.292,-215.697C844.639,-207.983 842.653,-198.712 840.81,-190.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="844.183,-189.149 838.665,-180.104 837.338,-190.616 844.183,-189.149"/>
+<!-- 16->22 -->
+<g id="edge42" class="edge"><title>16->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M673.279,-728.113C731.011,-719.162 820.701,-704.115 907.607,-683.955"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="908.43,-687.357 917.367,-681.666 906.832,-680.542 908.43,-687.357"/>
+</g>
+<!-- 17 -->
+<g id="node18" class="node"><title>17</title>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M577,-468C577,-468 501,-468 501,-468 495,-468 489,-462 489,-456 489,-456 489,-444 489,-444 489,-438 495,-432 501,-432 501,-432 577,-432 577,-432 583,-432 589,-438 589,-444 589,-444 589,-456 589,-456 589,-462 583,-468 577,-468"/>
+<text text-anchor="middle" x="539" y="-447.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
+</g>
+<!-- 17->8 -->
+<g id="edge18" class="edge"><title>17->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M523.921,-431.697C516.608,-423.305 507.69,-413.07 499.665,-403.861"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="502.114,-401.344 492.905,-396.104 496.836,-405.943 502.114,-401.344"/>
+</g>
+<!-- 18->9 -->
+<g id="edge20" class="edge"><title>18->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M388.357,-647.876C373.582,-638.724 355.209,-627.342 339.297,-617.485"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="341.093,-614.481 330.749,-612.19 337.407,-620.431 341.093,-614.481"/>
+</g>
+<!-- 18->10 -->
+<g id="edge22" class="edge"><title>18->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M428.607,-647.697C434.597,-639.474 441.876,-629.483 448.479,-620.421"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="451.478,-622.248 454.538,-612.104 445.821,-618.126 451.478,-622.248"/>
+</g>
+<!-- 19->9 -->
+<g id="edge19" class="edge"><title>19->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M497.206,-649.378C460.723,-639.163 412.756,-625.732 373.621,-614.774"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="374.447,-611.371 363.874,-612.045 372.56,-618.111 374.447,-611.371"/>
+</g>
+<!-- 19->10 -->
+<g id="edge21" class="edge"><title>19->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M531.742,-647.697C520.911,-638.881 507.582,-628.032 495.84,-618.474"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="497.979,-615.703 488.014,-612.104 493.56,-621.132 497.979,-615.703"/>
+</g>
+<!-- 20->11 -->
+<g id="edge24" class="edge"><title>20->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M899.722,-649.313C918.045,-641.265 936.359,-629.365 947,-612 955.359,-598.357 955.132,-589.779 947,-576 934.386,-554.628 909.727,-541.279 888.56,-533.324"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="889.422,-529.918 878.828,-529.94 887.123,-536.53 889.422,-529.918"/>
</g>
<!-- 21 -->
<g id="node22" class="node"><title>21</title>
-<path fill="none" stroke="#80d856" stroke-width="2" d="M1054,-324C1054,-324 974,-324 974,-324 968,-324 962,-318 962,-312 962,-312 962,-300 962,-300 962,-294 968,-288 974,-288 974,-288 1054,-288 1054,-288 1060,-288 1066,-294 1066,-300 1066,-300 1066,-312 1066,-312 1066,-318 1060,-324 1054,-324"/>
-<text text-anchor="middle" x="1014" y="-303.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
+<path fill="none" stroke="#56b9d8" stroke-width="2" d="M926,-612C926,-612 776,-612 776,-612 770,-612 764,-606 764,-600 764,-600 764,-588 764,-588 764,-582 770,-576 776,-576 776,-576 926,-576 926,-576 932,-576 938,-582 938,-588 938,-588 938,-600 938,-600 938,-606 932,-612 926,-612"/>
+<text text-anchor="middle" x="851" y="-591.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
</g>
-<!-- 21->9 -->
-<g id="edge24" class="edge"><title>21->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M998.839,-287.668C981.776,-268.746 952.678,-238.186 924,-216 907.558,-203.28 887.819,-191.241 871.112,-181.862"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="872.629,-178.702 862.182,-176.937 869.249,-184.831 872.629,-178.702"/>
+<!-- 20->21 -->
+<g id="edge40" class="edge"><title>20->21</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M844.978,-647.697C845.859,-639.983 846.919,-630.712 847.901,-622.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="851.387,-622.437 849.045,-612.104 844.432,-621.642 851.387,-622.437"/>
</g>
-<!-- 22 -->
-<g id="node23" class="node"><title>22</title>
-<path fill="none" stroke="#d8c356" stroke-width="2" d="M407,-612C407,-612 281,-612 281,-612 275,-612 269,-606 269,-600 269,-600 269,-588 269,-588 269,-582 275,-576 281,-576 281,-576 407,-576 407,-576 413,-576 419,-582 419,-588 419,-588 419,-600 419,-600 419,-606 413,-612 407,-612"/>
-<text text-anchor="middle" x="344" y="-591.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<!-- 28 -->
+<g id="node29" class="node"><title>28</title>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M780,-540C780,-540 692,-540 692,-540 686,-540 680,-534 680,-528 680,-528 680,-516 680,-516 680,-510 686,-504 692,-504 692,-504 780,-504 780,-504 786,-504 792,-510 792,-516 792,-516 792,-528 792,-528 792,-534 786,-540 780,-540"/>
+<text text-anchor="middle" x="736" y="-519.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+</g>
+<!-- 20->28 -->
+<g id="edge46" class="edge"><title>20->28</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M799.53,-647.827C783.272,-639.345 766.08,-627.537 755,-612 742.133,-593.959 737.662,-568.972 736.249,-550.065"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="739.741,-549.812 735.737,-540.002 732.75,-550.167 739.741,-549.812"/>
+</g>
+<!-- 21->11 -->
+<g id="edge23" class="edge"><title>21->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M851,-575.697C851,-567.983 851,-558.712 851,-550.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="854.5,-550.104 851,-540.104 847.5,-550.104 854.5,-550.104"/>
+</g>
+<!-- 21->28 -->
+<g id="edge45" class="edge"><title>21->28</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M822.868,-575.876C807.832,-566.724 789.133,-555.342 772.94,-545.485"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="774.602,-542.4 764.24,-540.19 770.962,-548.379 774.602,-542.4"/>
</g>
<!-- 22->11 -->
-<g id="edge26" class="edge"><title>22->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M342.764,-575.697C342.213,-567.983 341.551,-558.712 340.937,-550.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="344.425,-549.83 340.222,-540.104 337.443,-550.328 344.425,-549.83"/>
+<g id="edge25" class="edge"><title>22->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M970.876,-647.724C975.205,-628.573 978.916,-597.548 965,-576 948.17,-549.94 914.888,-536.48 888.609,-529.662"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="889.107,-526.183 878.57,-527.284 887.494,-532.994 889.107,-526.183"/>
</g>
-<!-- 23 -->
-<g id="node24" class="node"><title>23</title>
-<path fill="none" stroke="#d88d56" stroke-width="2" d="M238.5,-612C238.5,-612 151.5,-612 151.5,-612 145.5,-612 139.5,-606 139.5,-600 139.5,-600 139.5,-588 139.5,-588 139.5,-582 145.5,-576 151.5,-576 151.5,-576 238.5,-576 238.5,-576 244.5,-576 250.5,-582 250.5,-588 250.5,-588 250.5,-600 250.5,-600 250.5,-606 244.5,-612 238.5,-612"/>
-<text text-anchor="middle" x="195" y="-591.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
+<!-- 22->21 -->
+<g id="edge39" class="edge"><title>22->21</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M937.868,-647.876C922.832,-638.724 904.133,-627.342 887.94,-617.485"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="889.602,-614.4 879.24,-612.19 885.962,-620.379 889.602,-614.4"/>
+</g>
+<!-- 22->28 -->
+<g id="edge48" class="edge"><title>22->28</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M967.332,-647.807C967.882,-627.847 965.54,-595.215 947,-576 941.799,-570.609 861.991,-551.541 802.055,-537.821"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="802.775,-534.395 792.247,-535.582 801.217,-541.22 802.775,-534.395"/>
</g>
<!-- 23->12 -->
<g id="edge27" class="edge"><title>23->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M195,-575.697C195,-567.983 195,-558.712 195,-550.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="198.5,-550.104 195,-540.104 191.5,-550.104 198.5,-550.104"/>
-</g>
-<!-- 26 -->
-<g id="node27" class="node"><title>26</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M522.5,-540C522.5,-540 437.5,-540 437.5,-540 431.5,-540 425.5,-534 425.5,-528 425.5,-528 425.5,-516 425.5,-516 425.5,-510 431.5,-504 437.5,-504 437.5,-504 522.5,-504 522.5,-504 528.5,-504 534.5,-510 534.5,-516 534.5,-516 534.5,-528 534.5,-528 534.5,-534 528.5,-540 522.5,-540"/>
-<text text-anchor="middle" x="480" y="-519.5" font-family="sans" font-size="10.00">create_index_salmon</text>
-</g>
-<!-- 23->26 -->
-<g id="edge46" class="edge"><title>23->26</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M250.642,-578.334C253.806,-577.536 256.942,-576.753 260,-576 326.125,-559.727 345.31,-557.324 415.453,-540.091"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="416.35,-543.475 425.218,-537.678 414.67,-536.68 416.35,-543.475"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M846.292,-431.697C844.639,-423.983 842.653,-414.712 840.81,-406.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="844.183,-405.149 838.665,-396.104 837.338,-406.616 844.183,-405.149"/>
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<!-- 24 -->
<g id="node25" class="node"><title>24</title>
-<path fill="none" stroke="#56d85b" stroke-width="2" d="M668,-612C668,-612 558,-612 558,-612 552,-612 546,-606 546,-600 546,-600 546,-588 546,-588 546,-582 552,-576 558,-576 558,-576 668,-576 668,-576 674,-576 680,-582 680,-588 680,-588 680,-600 680,-600 680,-606 674,-612 668,-612"/>
-<text text-anchor="middle" x="613" y="-591.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+<path fill="none" stroke="#b6d856" stroke-width="2" d="M1054,-540C1054,-540 974,-540 974,-540 968,-540 962,-534 962,-528 962,-528 962,-516 962,-516 962,-510 968,-504 974,-504 974,-504 1054,-504 1054,-504 1060,-504 1066,-510 1066,-516 1066,-516 1066,-528 1066,-528 1066,-534 1060,-540 1054,-540"/>
+<text text-anchor="middle" x="1014" y="-519.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
</g>
-<!-- 24->13 -->
-<g id="edge28" class="edge"><title>24->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M613,-575.697C613,-567.983 613,-558.712 613,-550.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="616.5,-550.104 613,-540.104 609.5,-550.104 616.5,-550.104"/>
+<!-- 24->12 -->
+<g id="edge26" class="edge"><title>24->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M998.839,-503.668C981.776,-484.746 952.678,-454.186 924,-432 907.558,-419.28 887.819,-407.241 871.112,-397.862"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="872.629,-394.702 862.182,-392.937 869.249,-400.831 872.629,-394.702"/>
+</g>
+<!-- 25 -->
+<g id="node26" class="node"><title>25</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M407,-828C407,-828 281,-828 281,-828 275,-828 269,-822 269,-816 269,-816 269,-804 269,-804 269,-798 275,-792 281,-792 281,-792 407,-792 407,-792 413,-792 419,-798 419,-804 419,-804 419,-816 419,-816 419,-822 413,-828 407,-828"/>
+<text text-anchor="middle" x="344" y="-807.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
</g>
<!-- 25->14 -->
<g id="edge29" class="edge"><title>25->14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M688.06,-287.966C660.535,-278.185 625.783,-265.836 596.759,-255.524"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="597.749,-252.161 587.155,-252.111 595.406,-258.757 597.749,-252.161"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M342.764,-791.697C342.213,-783.983 341.551,-774.712 340.937,-766.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="344.425,-765.83 340.222,-756.104 337.443,-766.328 344.425,-765.83"/>
+</g>
+<!-- 26 -->
+<g id="node27" class="node"><title>26</title>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M238.5,-828C238.5,-828 151.5,-828 151.5,-828 145.5,-828 139.5,-822 139.5,-816 139.5,-816 139.5,-804 139.5,-804 139.5,-798 145.5,-792 151.5,-792 151.5,-792 238.5,-792 238.5,-792 244.5,-792 250.5,-798 250.5,-804 250.5,-804 250.5,-816 250.5,-816 250.5,-822 244.5,-828 238.5,-828"/>
+<text text-anchor="middle" x="195" y="-807.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
</g>
<!-- 26->15 -->
<g id="edge30" class="edge"><title>26->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M464.18,-503.697C456.43,-495.22 446.961,-484.864 438.476,-475.583"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="440.969,-473.123 431.638,-468.104 435.803,-477.846 440.969,-473.123"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M195,-791.697C195,-783.983 195,-774.712 195,-766.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="198.5,-766.104 195,-756.104 191.5,-766.104 198.5,-766.104"/>
+</g>
+<!-- 29 -->
+<g id="node30" class="node"><title>29</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M522.5,-756C522.5,-756 437.5,-756 437.5,-756 431.5,-756 425.5,-750 425.5,-744 425.5,-744 425.5,-732 425.5,-732 425.5,-726 431.5,-720 437.5,-720 437.5,-720 522.5,-720 522.5,-720 528.5,-720 534.5,-726 534.5,-732 534.5,-732 534.5,-744 534.5,-744 534.5,-750 528.5,-756 522.5,-756"/>
+<text text-anchor="middle" x="480" y="-735.5" font-family="sans" font-size="10.00">create_index_salmon</text>
</g>
-<!-- 26->16 -->
-<g id="edge32" class="edge"><title>26->16</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M498.045,-503.697C507.062,-495.05 518.118,-484.449 527.943,-475.027"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="530.367,-477.552 535.163,-468.104 525.522,-472.499 530.367,-477.552"/>
+<!-- 26->29 -->
+<g id="edge49" class="edge"><title>26->29</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M250.642,-794.334C253.806,-793.536 256.942,-792.753 260,-792 326.125,-775.727 345.31,-773.324 415.453,-756.091"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="416.35,-759.475 425.218,-753.678 414.67,-752.68 416.35,-759.475"/>
</g>
<!-- 27 -->
<g id="node28" class="node"><title>27</title>
-<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1001,-540C1001,-540 931,-540 931,-540 925,-540 919,-534 919,-528 919,-528 919,-516 919,-516 919,-510 925,-504 931,-504 931,-504 1001,-504 1001,-504 1007,-504 1013,-510 1013,-516 1013,-516 1013,-528 1013,-528 1013,-534 1007,-540 1001,-540"/>
-<text text-anchor="middle" x="966" y="-519.5" font-family="sans" font-size="10.00">create_index_star</text>
-</g>
-<!-- 27->17 -->
-<g id="edge34" class="edge"><title>27->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M935.911,-503.876C919.68,-494.639 899.458,-483.131 882.029,-473.212"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="883.627,-470.094 873.205,-468.19 880.165,-476.178 883.627,-470.094"/>
-</g>
-<!-- 27->19 -->
-<g id="edge38" class="edge"><title>27->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M966,-503.697C966,-495.983 966,-486.712 966,-478.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="969.5,-478.104 966,-468.104 962.5,-478.104 969.5,-478.104"/>
-</g>
-<!-- 27->21 -->
-<g id="edge41" class="edge"><title>27->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M993.34,-503.775C1005.11,-494.718 1017.62,-482.478 1024,-468 1043.27,-424.297 1032.42,-367.371 1023.04,-334.235"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1026.3,-332.935 1020.08,-324.359 1019.6,-334.943 1026.3,-332.935"/>
-</g>
-<!-- 28 -->
-<g id="node29" class="node"><title>28</title>
-<path fill="none" stroke="#b6d856" stroke-width="2" d="M695.5,-396C695.5,-396 574.5,-396 574.5,-396 568.5,-396 562.5,-390 562.5,-384 562.5,-384 562.5,-372 562.5,-372 562.5,-366 568.5,-360 574.5,-360 574.5,-360 695.5,-360 695.5,-360 701.5,-360 707.5,-366 707.5,-372 707.5,-372 707.5,-384 707.5,-384 707.5,-390 701.5,-396 695.5,-396"/>
-<text text-anchor="middle" x="635" y="-375.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
-</g>
-<!-- 28->25 -->
-<g id="edge43" class="edge"><title>28->25</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M659.707,-359.876C672.669,-350.893 688.728,-339.763 702.765,-330.034"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="704.972,-332.763 711.198,-324.19 700.985,-327.009 704.972,-332.763"/>
+<path fill="none" stroke="#567bd8" stroke-width="2" d="M668,-828C668,-828 558,-828 558,-828 552,-828 546,-822 546,-816 546,-816 546,-804 546,-804 546,-798 552,-792 558,-792 558,-792 668,-792 668,-792 674,-792 680,-798 680,-804 680,-804 680,-816 680,-816 680,-822 674,-828 668,-828"/>
+<text text-anchor="middle" x="613" y="-807.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+</g>
+<!-- 27->16 -->
+<g id="edge31" class="edge"><title>27->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M613,-791.697C613,-783.983 613,-774.712 613,-766.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="616.5,-766.104 613,-756.104 609.5,-766.104 616.5,-766.104"/>
+</g>
+<!-- 28->17 -->
+<g id="edge32" class="edge"><title>28->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M688.06,-503.966C660.535,-494.185 625.783,-481.836 596.759,-471.524"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="597.749,-468.161 587.155,-468.111 595.406,-474.757 597.749,-468.161"/>
+</g>
+<!-- 29->18 -->
+<g id="edge33" class="edge"><title>29->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M464.18,-719.697C456.43,-711.22 446.961,-700.864 438.476,-691.583"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="440.969,-689.123 431.638,-684.104 435.803,-693.846 440.969,-689.123"/>
+</g>
+<!-- 29->19 -->
+<g id="edge35" class="edge"><title>29->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M498.045,-719.697C507.062,-711.05 518.118,-700.449 527.943,-691.027"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="530.367,-693.552 535.163,-684.104 525.522,-688.499 530.367,-693.552"/>
+</g>
+<!-- 30 -->
+<g id="node31" class="node"><title>30</title>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1001,-756C1001,-756 931,-756 931,-756 925,-756 919,-750 919,-744 919,-744 919,-732 919,-732 919,-726 925,-720 931,-720 931,-720 1001,-720 1001,-720 1007,-720 1013,-726 1013,-732 1013,-732 1013,-744 1013,-744 1013,-750 1007,-756 1001,-756"/>
+<text text-anchor="middle" x="966" y="-735.5" font-family="sans" font-size="10.00">create_index_star</text>
+</g>
+<!-- 30->20 -->
+<g id="edge37" class="edge"><title>30->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M935.911,-719.876C919.68,-710.639 899.458,-699.131 882.029,-689.212"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="883.627,-686.094 873.205,-684.19 880.165,-692.178 883.627,-686.094"/>
+</g>
+<!-- 30->22 -->
+<g id="edge41" class="edge"><title>30->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M966,-719.697C966,-711.983 966,-702.712 966,-694.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="969.5,-694.104 966,-684.104 962.5,-694.104 969.5,-694.104"/>
+</g>
+<!-- 30->24 -->
+<g id="edge44" class="edge"><title>30->24</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M993.34,-719.775C1005.11,-710.718 1017.62,-698.478 1024,-684 1043.27,-640.297 1032.42,-583.371 1023.04,-550.235"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1026.3,-548.935 1020.08,-540.359 1019.6,-550.943 1026.3,-548.935"/>
+</g>
+<!-- 31 -->
+<g id="node32" class="node"><title>31</title>
+<path fill="none" stroke="#59d856" stroke-width="2" d="M695.5,-612C695.5,-612 574.5,-612 574.5,-612 568.5,-612 562.5,-606 562.5,-600 562.5,-600 562.5,-588 562.5,-588 562.5,-582 568.5,-576 574.5,-576 574.5,-576 695.5,-576 695.5,-576 701.5,-576 707.5,-582 707.5,-588 707.5,-588 707.5,-600 707.5,-600 707.5,-606 701.5,-612 695.5,-612"/>
+<text text-anchor="middle" x="635" y="-591.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+</g>
+<!-- 31->28 -->
+<g id="edge47" class="edge"><title>31->28</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M659.707,-575.876C672.669,-566.893 688.728,-555.763 702.765,-546.034"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="704.972,-548.763 711.198,-540.19 700.985,-543.009 704.972,-548.763"/>
</g>
</g>
</svg>
diff --git a/install/environment.dev.yml b/install/environment.dev.yml
index ea44dfbcfb7f02409682d231014e528c2845cb83..ab5c30ac6c60c998193981c084150d4bc907b41d 100644
--- a/install/environment.dev.yml
+++ b/install/environment.dev.yml
@@ -1,4 +1,4 @@
-name: rnaseq_pipeline
+name: rhea
channels:
- bioconda
- conda-forge
diff --git a/install/environment.root.yml b/install/environment.root.yml
index 9c6d56dd4a0ab2d3a1f7907549a71053c35a4cd0..7017feb85a963093898030ae135b094244c4774d 100644
--- a/install/environment.root.yml
+++ b/install/environment.root.yml
@@ -1,4 +1,4 @@
-name: rnaseq_pipeline
+name: rhea
channels:
- conda-forge
- defaults
diff --git a/install/environment.yml b/install/environment.yml
index dd6b5d5061a9186dfa6bb37f5f9caf0a8886c06b..4fa641ab259484f747f4af4d70f5464d41649aab 100644
--- a/install/environment.yml
+++ b/install/environment.yml
@@ -1,4 +1,4 @@
-name: rnaseq_pipeline
+name: rhea
channels:
- defaults
dependencies:
diff --git a/pipeline_documentation.md b/pipeline_documentation.md
index 18a64881b281385ca4d370e95683d5efa2af1263..41bc09574a0795e94593744c4be876cfc55f52f8 100644
--- a/pipeline_documentation.md
+++ b/pipeline_documentation.md
@@ -1,4 +1,4 @@
-# RNAseq pipeline documentation
+# Rhea workflow documentation
This document describes the individual rules of the pipeline for information purposes. For instructions on installation and usage please refer to the [README](README.md).
## Overview
@@ -14,11 +14,16 @@ This document describes the individual rules of the pipeline for information pur
* **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**
+* **prepare_files_for_report**
+* **prepare_MultiQC_config**
+* **MULTIQC_report**
### Sequencing mode specific
* **(pe_)fastqc**
@@ -160,6 +165,22 @@ Given a set of BAM files and a gene annotation BED file, calculates the Transcri
+#### merge_TIN_scores
+Concatenates the tsv files of all samples into one wider table.
+
+**Input:** TIN score tsv files per sample
+**Output:** TIN score tsv file for all samples
+
+
+
+#### plot_TIN_scores
+Generates sample-wise [boxplots](https://en.wikipedia.org/wiki/Box_plot) of TIN scores.
+
+**Input:** TIN score tsv file for all samples
+**Output:** .pdf and .png files with boxplots
+
+
+
#### salmon_quantmerge_genes
Merge the salmon quantification *gene* results for all samples of same sequencing mode into a single file. Do this for tpm and number of reads separately.
@@ -197,7 +218,29 @@ The main output of ALFA are two plots, `ALFA_Biotypes.pdf` and `ALFA_Categories.
Combine the output of all samples into one plot generated by [ALFA](https://github.com/biocompibens/ALFA).
**Input:** ALFA_feature_counts.tsv from each sample in `samples.tsv`
-**Output:** ALFA_Biotypes.pdf and ALFA_Categories.pdf for all samples together
+**Output:** ALFA_Biotypes.pdf and ALFA_Categories.pdf for all samples together
+
+
+
+#### prepare_files_for_report
+This is an internal rule with `run` directive. It gathers all the output files, restructures the `log` and `results` directories and modifies some `stdout` and `stderr` streams of previous rules for proper parsing of sample names in the final report.
+
+
+
+#### prepare_MultiQC_config
+Prepares a dedicated config file for [MultiQC](https://multiqc.info/).
+
+**Input:** Currently directories created during `prepare_files_for_report` serve as input.
+**Output:** Config file in .yaml format
+
+
+
+#### MULTIQC_report
+Creates an interactive report after the pipeline is finished. [MultiQC](https://multiqc.info/) gathers results and logs after distinct bioinformatics tools, parses them and presents the output graphically in an HTML file.
+
+**Input:** Config file fort MultiQC in .yaml format
+**Output:** Directory with automatically generated HTML report
+
### Sequencing mode specific rules
@@ -315,3 +358,4 @@ Spliced Transcripts Alignment to a Reference; Read the [Publication](https://www
* -l: fragment length, user specified as `mean`
* -s: fragment length SD, user specified as `sd`
+
diff --git a/tests/test_alfa/test.sh b/tests/test_alfa/test.sh
index 280749cde715c6bc58b2b56a7cbb13560589a8e1..2f45621e5b73f2147c7e46b9543cb72f5addae89 100755
--- a/tests/test_alfa/test.sh
+++ b/tests/test_alfa/test.sh
@@ -31,7 +31,7 @@ snakemake \
--printshellcmds \
--rerun-incomplete \
--use-singularity \
- --singularity-args="--bind ${PWD}/../input_files" \
+ --singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
--verbose \
results/ALFA/ALFA_plots.Categories.pdf
diff --git a/tests/test_integration_workflow/expected_output.files b/tests/test_integration_workflow/expected_output.files
index 490153d374d390bcdc670c095e32acabe11c29f0..796a9131b20194cca55d2ee7cf9789f62c9bcd7a 100644
--- a/tests/test_integration_workflow/expected_output.files
+++ b/tests/test_integration_workflow/expected_output.files
@@ -16,66 +16,66 @@ 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/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_adapters_mate1.fastq
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_adapters_mate2.fastq
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_polya_mate1.fastq
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_polya_mate2.fastq
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_SJ.out.tab
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/fastqc_data.txt
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/fastqc.fo
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/summary.txt
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/adapter_content.png
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/duplication_levels.png
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_n_content.png
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_quality.png
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_sequence_content.png
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_sequence_gc_content.png
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_sequence_quality.png
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_tile_quality.png
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/sequence_length_distribution.png
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/fastqc_data.txt
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/fastqc.fo
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/summary.txt
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/adapter_content.png
-results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/duplication_levels.png
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diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
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-c1254a0bae19ac3ffc39f73099ffcf2b results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
-bcccf679a8c083d01527514c9f5680a0 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.minus.bg
-ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.plus.bg
\ No newline at end of file
+c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
+c266d31e0a2ad84975cb9de335891e64 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.minus.bg
+0139e75ddbfe6eb081c2c2d9b9108ab4 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.plus.bg
+c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
+bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.minus.bg
+ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.plus.bg
diff --git a/tests/test_integration_workflow/test.local.sh b/tests/test_integration_workflow/test.local.sh
index 5f10636dd17051d88c85320ad28e309cfdd337d1..ac6e45ec44898fb8204019cc26e3d85faaaecb62 100755
--- a/tests/test_integration_workflow/test.local.sh
+++ b/tests/test_integration_workflow/test.local.sh
@@ -29,7 +29,7 @@ snakemake \
--printshellcmds \
--rerun-incomplete \
--use-singularity \
- --singularity-args="--bind ${PWD}/../input_files" \
+ --singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
--verbose
# Check md5 sum of some output files
@@ -55,7 +55,7 @@ md5sum --check "expected_output.md5"
echo "Verifying STAR output"
result=$(bedtools intersect -F 1 -v -bed \
-a ../input_files/synthetic.mate_1.bed \
- -b results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam \
+ -b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam \
| wc -l)
if [ $result != "0" ]; then
echo "Alignments for mate 1 reads are not consistent with ground truth"
@@ -63,7 +63,7 @@ if [ $result != "0" ]; then
fi
result=$(bedtools intersect -F 1 -v -bed \
-a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \
- -b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam \
+ -b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam \
| wc -l)
if [ $result != "0" ]; then
echo "Alignments for mate 1 reads are not consistent with ground truth"
@@ -73,9 +73,9 @@ fi
# Check whether Salmon assigns reads to expected genes
echo "Verifying Salmon output"
diff \
- <(cat results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+ <(cat results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
<(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
diff \
- <(cat results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+ <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/synthetic_10_reads_paired_synthetic_10_reads_paired/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
<(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
diff --git a/tests/test_integration_workflow/test.slurm.sh b/tests/test_integration_workflow/test.slurm.sh
index f67878a809a4b71dc56ce2c40fc28153c0947faf..bc06d8e0ef4d40d8960f0719715fe4330a85c639 100755
--- a/tests/test_integration_workflow/test.slurm.sh
+++ b/tests/test_integration_workflow/test.slurm.sh
@@ -31,7 +31,7 @@ snakemake \
--printshellcmds \
--rerun-incomplete \
--use-singularity \
- --singularity-args="--bind ${PWD}/../input_files" \
+ --singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
--verbose
# Check md5 sum of some output files
@@ -57,7 +57,7 @@ md5sum --check "expected_output.md5"
echo "Verifying STAR output"
result=$(bedtools intersect -F 1 -v -bed \
-a ../input_files/synthetic.mate_1.bed \
- -b results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam \
+ -b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam \
| wc -l)
if [ $result != "0" ]; then
echo "Alignments for mate 1 reads are not consistent with ground truth"
@@ -65,7 +65,7 @@ if [ $result != "0" ]; then
fi
result=$(bedtools intersect -F 1 -v -bed \
-a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \
- -b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam \
+ -b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam \
| wc -l)
if [ $result != "0" ]; then
echo "Alignments for mate 1 reads are not consistent with ground truth"
@@ -75,9 +75,9 @@ fi
# Check whether Salmon assigns reads to expected genes
echo "Verifying Salmon output"
diff \
- <(cat results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+ <(cat results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
<(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
diff \
- <(cat results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+ <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/synthetic_10_reads_paired_synthetic_10_reads_paired/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
<(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index 72685e3cc85d32c8a5d221df40bc6075ff9426e6..a642c65ba093b4798c03fae59a51c091266728a6 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -183,7 +183,7 @@ rule pe_remove_polya_cutadapt:
-o {output.reads1} \
-p {output.reads2} \
{input.reads1} \
- {input.reads2};) \
+ {input.reads2}) \
1> {log.stdout} 2>{log.stderr}"
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index 3e09fc0c00b96ee3b2ac4f7756e6914fc5d6c656..d0b844544718f3df3d02e2343ae7518257741bd3 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -84,7 +84,7 @@ rule remove_adapters_cutadapt:
-a {params.adapters_3} \
-g {params.adapters_5} \
-o {output.reads} \
- {input.reads};) \
+ {input.reads}) \
1> {log.stdout} 2> {log.stderr}"