diff --git a/README.md b/README.md
index 9fd71c2dbf490bcd0c4e1b4fd56b87fc0645161c..c77c22f7455bb8501e22c012e2540485c11eac4f 100644
--- a/README.md
+++ b/README.md
@@ -173,7 +173,6 @@ your run.
```bash
cat << "EOF" > run.sh
#!/bin/bash
- mkdir -p logs/local_log
snakemake \
--snakefile="../../snakemake/Snakefile" \
--configfile="config.yaml" \
diff --git a/Snakefile b/Snakefile
index 17137c97568138d1787f4360a49d0211494520e4..aa8c3475f78fe73c4cc4242bb8eeaf2fa3e56231 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1,160 +1,255 @@
-################################################################################
-### python modules
-################################################################################
+"""General purpose RNA-Seq analysis pipeline developed by the Zavolan Lab"""
import os
import sys
-import pandas as pd
-############################
+import pandas as pd
-samples_table = pd.read_csv(config["samples"], header=0, index_col=0, comment='#', engine='python', sep="\t")
+# Get sample table
+samples_table = pd.read_csv(
+ config['samples'],
+ header=0,
+ index_col=0,
+ comment='#',
+ engine='python',
+ sep="\t",
+)
+# Global config
localrules: finish
-##################################################################################
-# Execution dependend on sequencing mode
-##################################################################################
-
-include: os.path.join('workflow', 'rules', 'paired_end.snakefile.smk')
-include: os.path.join('workflow', 'rules', 'single_end.snakefile.smk')
+# Create log directories
+os.makedirs(
+ os.path.join(
+ os.getcwd(),
+ config['log_dir'],
+ ),
+ exist_ok=True,
+)
+if cluster_config:
+ os.makedirs(
+ os.path.join(
+ os.getcwd(),
+ os.path.dirname(cluster_config['__default__']['out']),
+ ),
+ exist_ok=True,
+ )
-#################################################################################
-### Final rule
-#################################################################################
+# Include subworkflows
+include: os.path.join("workflow", "rules", "paired_end.snakefile.smk")
+include: os.path.join("workflow", "rules", "single_end.snakefile.smk")
+# Final rule
rule finish:
- 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)]),
- salmon_gn_estimates = expand(os.path.join(config["output_dir"],"{seqmode}","{sample}","salmon_quant","quant.genes.sf"),
- 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_score = expand(os.path.join(config["output_dir"], "{seqmode}", "{sample}", "TIN", "TIN_score.tsv"),
- zip,
- sample= [i for i in list(samples_table.index.values)],
- seqmode= [samples_table.loc[i,"seqmode"] for i in list(samples_table.index.values)]),
+ """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)
+ ]
+ ),
+ salmon_gn_estimates = expand(
+ os.path.join(
+ config['output_dir'],
+ "{seqmode}",
+ "{sample}",
+ "salmon_quant",
+ "quant.genes.sf",
+ ),
+ 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_score = expand(
+ os.path.join(
+ config['output_dir'],
+ "{seqmode}",
+ "{sample}",
+ "TIN",
+ "TIN_score.tsv",
+ ),
+ zip,
+ sample=[i for i in list(samples_table.index.values)],
+ seqmode=[
+ samples_table.loc[i, 'seqmode']
+ for i in list(samples_table.index.values)
+ ]
+ ),
rule create_index_star:
- ''' Create index using STAR'''
- input:
- genome =lambda wildcards: samples_table["genome"][samples_table["organism"]==wildcards.organism][0],
- gtf =lambda wildcards: samples_table["gtf"][samples_table["organism"]==wildcards.organism][0]
- output:
- chromosome_info = os.path.join(
- config["star_indexes"],
- "{organism}",
- "{index_size}",
- "STAR_index",
- "chrNameLength.txt"),
- chromosomes_names = os.path.join(
- config["star_indexes"],
- "{organism}",
- "{index_size}",
- "STAR_index",
- "chrName.txt")
- params:
- output_dir = os.path.join(
- config["star_indexes"],
- "{organism}",
- "{index_size}",
- "STAR_index"),
- outFileNamePrefix = os.path.join(
- config["star_indexes"],
- "{organism}",
- "{index_size}",
- "STAR_index/STAR_"),
- sjdbOverhang = "{index_size}"
- singularity:
- "docker://zavolab/star:2.6.0a"
- threads: 12
- log:
- os.path.join( config["local_log"], "{organism}_{index_size}_create_index_star.log")
- shell:
- "(mkdir -p {params.output_dir}; \
- chmod -R 777 {params.output_dir}; \
- STAR \
- --runMode genomeGenerate \
- --sjdbOverhang {params.sjdbOverhang} \
- --genomeDir {params.output_dir} \
- --genomeFastaFiles {input.genome} \
- --runThreadN {threads} \
- --outFileNamePrefix {params.outFileNamePrefix} \
- --sjdbGTFfile {input.gtf}) &> {log}"
+ """Create index for STAR alignments"""
+ input:
+ genome = lambda wildcards:
+ samples_table['genome'][
+ samples_table['organism'] == wildcards.organism
+ ][0],
+ gtf = lambda wildcards:
+ samples_table['gtf'][
+ samples_table['organism'] == wildcards.organism
+ ][0],
+ output:
+ chromosome_info = os.path.join(
+ config['star_indexes'],
+ "{organism}",
+ "{index_size}",
+ "STAR_index",
+ "chrNameLength.txt",
+ ),
+ chromosomes_names = os.path.join(
+ config['star_indexes'],
+ "{organism}",
+ "{index_size}",
+ "STAR_index",
+ "chrName.txt",
+ ),
+ params:
+ output_dir = os.path.join(
+ config['star_indexes'],
+ "{organism}",
+ "{index_size}",
+ "STAR_index",
+ ),
+ outFileNamePrefix = os.path.join(
+ config['star_indexes'],
+ "{organism}",
+ "{index_size}",
+ "STAR_index/STAR_",
+ ),
+ sjdbOverhang = "{index_size}",
+ singularity:
+ "docker://zavolab/star:2.6.0a"
+ threads: 12
+ log:
+ os.path.join(
+ config['log_dir'],
+ "{organism}_{index_size}_create_index_star.log",
+ )
+ shell:
+ "(mkdir -p {params.output_dir}; \
+ chmod -R 777 {params.output_dir}; \
+ STAR \
+ --runMode genomeGenerate \
+ --sjdbOverhang {params.sjdbOverhang} \
+ --genomeDir {params.output_dir} \
+ --genomeFastaFiles {input.genome} \
+ --runThreadN {threads} \
+ --outFileNamePrefix {params.outFileNamePrefix} \
+ --sjdbGTFfile {input.gtf}) &> {log}"
rule create_index_salmon:
- '''Create index for salmon quantification'''
- input:
- transcriptome = lambda wildcards: samples_table['tr_fasta_filtered'][samples_table["organism"]==wildcards.organism][0]
- output:
- index = directory(os.path.join(
- config["salmon_indexes"],
- "{organism}",
- "{kmer}",
- "salmon.idx"))
-
- params:
- kmerLen = "{kmer}"
- singularity:
- "docker://zavolab/salmon:0.11.0"
- log:
- os.path.join(config["local_log"], "{organism}_{kmer}_create_index_salmon.log")
- threads: 8
- shell:
- "(salmon index \
- --transcripts {input.transcriptome} \
- --index {output.index} \
- --kmerLen {params.kmerLen} \
- --threads {threads}) &> {log}"
+ """Create index for Salmon quantification"""
+ input:
+ transcriptome = lambda wildcards:
+ samples_table['tr_fasta_filtered'][
+ samples_table['organism'] == wildcards.organism
+ ][0]
+ output:
+ index = directory(
+ os.path.join(
+ config['salmon_indexes'],
+ "{organism}",
+ "{kmer}",
+ "salmon.idx",
+ )
+ ),
+ params:
+ kmerLen = "{kmer}",
+ singularity:
+ "docker://zavolab/salmon:0.11.0"
+ log:
+ os.path.join(
+ config['log_dir'],
+ "{organism}_{kmer}_create_index_salmon.log"
+ )
+ threads: 8
+ shell:
+ "(salmon index \
+ --transcripts {input.transcriptome} \
+ --index {output.index} \
+ --kmerLen {params.kmerLen} \
+ --threads {threads}) &> {log}"
rule create_index_kallisto:
- '''Create index for running Kallisto'''
- input:
- transcriptome = lambda wildcards: samples_table['tr_fasta_filtered'][samples_table["organism"]==wildcards.organism][0]
- output:
- index = os.path.join(
- config["kallisto_indexes"],
- "{organism}",
- "kallisto.idx")
- params:
- output_dir = os.path.join(
- config["kallisto_indexes"],
- "{organism}")
- singularity:
- "docker://zavolab/kallisto:0.46.1"
- log:
- os.path.join(config["local_log"], "{organism}_create_index_kallisto.log")
- shell:
- "(mkdir -p {params.output_dir}; \
- chmod -R 777 {params.output_dir}; \
- kallisto index -i {output.index} {input.transcriptome}) &> {log}"
+ """Create index for Kallisto quantification"""
+ input:
+ transcriptome = lambda wildcards:
+ samples_table['tr_fasta_filtered'][
+ samples_table['organism'] == wildcards.organism
+ ][0],
+ output:
+ index = os.path.join(
+ config['kallisto_indexes'],
+ "{organism}",
+ "kallisto.idx",
+ ),
+ params:
+ output_dir = os.path.join(
+ config['kallisto_indexes'],
+ "{organism}",
+ ),
+ singularity:
+ "docker://zavolab/kallisto:0.46.1"
+ log:
+ os.path.join(
+ config['log_dir'],
+ "{organism}_create_index_kallisto.log"
+ )
+ shell:
+ "(mkdir -p {params.output_dir}; \
+ chmod -R 777 {params.output_dir}; \
+ kallisto index -i {output.index} {input.transcriptome}) &> {log}"
rule extract_transcripts_as_bed12:
- ''' Extract transcripts: from GTF into BED12 format'''
- input:
- gtf =lambda wildcards: samples_table["gtf"][0]
- output:
- bed12 = os.path.join(
- config["output_dir"],
- "full_transcripts_protein_coding.bed")
- singularity:
- "docker://zavolab/gtf_transcript_type_to_bed12:0.1.0"
- threads: 1
- log:
- os.path.join( config["local_log"], "extract_transcripts_as_bed12.log")
- shell:
- "gtf_transcript_type_to_bed12.pl \
+ """Convert transcripts to BED12 format"""
+ input:
+ gtf = lambda wildcards:
+ samples_table['gtf'][0],
+ output:
+ bed12 = os.path.join(
+ config['output_dir'],
+ "full_transcripts_protein_coding.bed",
+ ),
+ singularity:
+ "docker://zavolab/gtf_transcript_type_to_bed12:0.1.0"
+ threads: 1
+ log:
+ os.path.join(
+ config['log_dir'],
+ "extract_transcripts_as_bed12.log",
+ )
+ shell:
+ "gtf_transcript_type_to_bed12.pl \
--anno={input.gtf} \
--type=protein_coding \
1> {output.bed12} \
@@ -162,39 +257,48 @@ rule extract_transcripts_as_bed12:
rule calculate_TIN_scores:
- '''Calculate TIN score'''
- input:
- bai = os.path.join(
- config["output_dir"],
- "{seqmode}",
- "{sample}",
- "map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam.bai"),
- transcripts_bed12 = os.path.join(
- config["output_dir"],
- "full_transcripts_protein_coding.bed")
- output:
- TIN_score = os.path.join(
- config["output_dir"],
- "{seqmode}",
- "{sample}",
- "TIN",
- "TIN_score.tsv")
- params:
- bam = os.path.join(
- config["output_dir"],
- "{seqmode}",
- "{sample}",
- "map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam"),
- sample = "{sample}"
- log:
- os.path.join(config["local_log"], "{seqmode}", "{sample}", "calculate_TIN_scores.log")
- threads: 8
- singularity:
- "docker://zavolab/tin_score_calculation:0.1.0"
- shell:
- "tin_score_calculation.py \
+ """Caluclate transcript integrity (TIN) score"""
+ input:
+ bai = os.path.join(
+ config['output_dir'],
+ "{seqmode}",
+ "{sample}",
+ "map_genome",
+ "{sample}_Aligned.sortedByCoord.out.bam.bai"
+ ),
+ transcripts_bed12 = os.path.join(
+ config['output_dir'],
+ "full_transcripts_protein_coding.bed"
+ ),
+ output:
+ TIN_score = os.path.join(
+ config['output_dir'],
+ "{seqmode}",
+ "{sample}",
+ "TIN",
+ "TIN_score.tsv",
+ ),
+ params:
+ bam = os.path.join(
+ config['output_dir'],
+ "{seqmode}",
+ "{sample}",
+ "map_genome",
+ "{sample}_Aligned.sortedByCoord.out.bam"
+ ),
+ sample = "{sample}",
+ log:
+ os.path.join(
+ config['log_dir'],
+ "{seqmode}",
+ "{sample}",
+ "calculate_TIN_scores.log",
+ )
+ threads: 8
+ singularity:
+ "docker://zavolab/tin_score_calculation:0.1.0"
+ shell:
+ "tin_score_calculation.py \
-i {params.bam} \
-r {input.transcripts_bed12} \
-c 0 \
diff --git a/scripts/labkey_to_snakemake.py b/scripts/labkey_to_snakemake.py
index d39db9c8878acdbbe1b110ba29864076ed8e5d5d..b6b9569b15d669afa97e785ff2bc83f9360351c8 100755
--- a/scripts/labkey_to_snakemake.py
+++ b/scripts/labkey_to_snakemake.py
@@ -305,12 +305,12 @@ def main():
# Read file and infer read size for sjdbovwerhang
with open(options.config_file, 'w') as config_file:
config_file.write('''---
- output_dir: "results"
- local_log: "local_log"
- star_indexes: "results/star_indexes"
- kallisto_indexes: "results/kallisto_indexes"
samples: "'''+ options.samples_table + '''"
- salmon_indexes: "results/salmon_indexes"
+ output_dir: "results/"
+ log_dir: "logs/"
+ kallisto_indexes: "results/kallisto_indexes/"
+ salmon_indexes: "results/salmon_indexes/"
+ star_indexes: "results/star_indexes/"
...''')
sys.stdout.write('Create snakemake table finished successfully...\n')
diff --git a/tests/input_files/cluster.json b/tests/input_files/cluster.json
index eaafcd3d52f53b015f6e4f8b1cde4e2838cd6b02..f0456181eb00ec2ee961050096d07b6422c48930 100644
--- a/tests/input_files/cluster.json
+++ b/tests/input_files/cluster.json
@@ -6,7 +6,7 @@
"threads": "1",
"mem": "4G",
"name": "{rule}.{wildcards}",
- "out": "$PWD/logs/cluster_log/{rule}.{wildcards}-%j-%N.out"
+ "out": "logs/cluster/{rule}.{wildcards}-%j-%N.out"
},
"generate_segemehl_index_other_RNAs":
{
diff --git a/tests/input_files/config.yaml b/tests/input_files/config.yaml
index 7697b12bf284d2c9c819610838b64843c8290bc1..b0a3f41c4216d08e4528f30cc82be02f0bb045db 100644
--- a/tests/input_files/config.yaml
+++ b/tests/input_files/config.yaml
@@ -1,8 +1,8 @@
---
- output_dir: "results"
- local_log: "local_log"
- star_indexes: "results/star_indexes"
- kallisto_indexes: "results/kallisto_indexes"
samples: "../input_files/samples.tsv"
- salmon_indexes: "results/salmon_indexes"
+ output_dir: "results/"
+ log_dir: "logs/"
+ kallisto_indexes: "results/kallisto_indexes/"
+ salmon_indexes: "results/salmon_indexes/"
+ star_indexes: "results/star_indexes/"
...
diff --git a/tests/test_create_dag_image/test.sh b/tests/test_create_dag_image/test.sh
index 0732292b15fe05802e9a7ef2a93f69e7c1b0ade9..afd8de4c0c0ca2cb86c3773c68477729a5395b37 100755
--- a/tests/test_create_dag_image/test.sh
+++ b/tests/test_create_dag_image/test.sh
@@ -4,6 +4,7 @@
cleanup () {
rc=$?
rm -rf .snakemake
+ rm -rf logs/
cd $user_dir
echo "Exit status: $rc"
}
diff --git a/tests/test_create_rule_graph/test.sh b/tests/test_create_rule_graph/test.sh
index b232a2e53b840e99708010cd98e2dc07edf3f4ad..51e538324c23a9514093427d7cd4db1a6a7123b2 100755
--- a/tests/test_create_rule_graph/test.sh
+++ b/tests/test_create_rule_graph/test.sh
@@ -4,6 +4,7 @@
cleanup () {
rc=$?
rm -rf .snakemake
+ rm -rf logs/
cd $user_dir
echo "Exit status: $rc"
}
diff --git a/tests/test_integration_workflow/test.local.sh b/tests/test_integration_workflow/test.local.sh
index 42e02fa41d021c0ffc7b7bcb33a02d18518f8dfd..ec650632cdc438ecc8e41e2e2e50e9e5193d95da 100755
--- a/tests/test_integration_workflow/test.local.sh
+++ b/tests/test_integration_workflow/test.local.sh
@@ -5,7 +5,6 @@ cleanup () {
rc=$?
rm -rf .java/
rm -rf .snakemake/
- rm -rf local_log/
rm -rf logs/
rm -rf results/
cd $user_dir
@@ -20,7 +19,6 @@ set -x # facilitates debugging by printing out executed commands
user_dir=$PWD
script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
cd $script_dir
-mkdir -p logs/local_log
# Run tests
snakemake \
diff --git a/tests/test_integration_workflow/test.slurm.sh b/tests/test_integration_workflow/test.slurm.sh
index 67df1e9cc6929318c63d6081d7d19e4c5e133cea..00aacd131ccff4c3cc1896a2db91a852c57ea841 100755
--- a/tests/test_integration_workflow/test.slurm.sh
+++ b/tests/test_integration_workflow/test.slurm.sh
@@ -5,7 +5,6 @@ cleanup () {
rc=$?
rm -rf .java/
rm -rf .snakemake/
- rm -rf local_log/
rm -rf logs/
rm -rf results/
cd $user_dir
@@ -20,8 +19,6 @@ set -x # facilitates debugging by printing out executed commands
user_dir=$PWD
script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
cd $script_dir
-mkdir -p logs/cluster_log
-mkdir -p logs/local_log
# Run tests
snakemake \
diff --git a/tests/test_scripts_labkey_to_snakemake_api/expected_output.md5 b/tests/test_scripts_labkey_to_snakemake_api/expected_output.md5
index 1dcb38fb810a501c33629ba2105aaed0794bca15..90bb3be03674c8c58697c0d1e488023d342d7772 100644
--- a/tests/test_scripts_labkey_to_snakemake_api/expected_output.md5
+++ b/tests/test_scripts_labkey_to_snakemake_api/expected_output.md5
@@ -1,2 +1,2 @@
-95fb0448dc6871cb415012d254260c5a config.yaml
+ba5ae0649d1fb82d94f8d19481498ffd config.yaml
9aece9e4acb17143b5e8f627968e03a5 samples.tsv
diff --git a/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5 b/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5
index 1dcb38fb810a501c33629ba2105aaed0794bca15..90bb3be03674c8c58697c0d1e488023d342d7772 100644
--- a/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5
+++ b/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5
@@ -1,2 +1,2 @@
-95fb0448dc6871cb415012d254260c5a config.yaml
+ba5ae0649d1fb82d94f8d19481498ffd config.yaml
9aece9e4acb17143b5e8f627968e03a5 samples.tsv
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index 53ef308fe85833f95f128e4b8b4c4e2ef4c298e7..1d1f7c0d3dd44b9d31a60159a5a5dd3680da4675 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -13,7 +13,7 @@ rule pe_fastqc:
singularity:
"docker://zavolab/fastqc:0.11.8"
log:
- os.path.join(config["local_log"],"paired_end", "{sample}", "fastqc.log")
+ os.path.join(config["log_dir"],"paired_end", "{sample}", "fastqc.log")
shell:
"(mkdir -p {output.outdir1}; \
mkdir -p {output.outdir2}; \
@@ -51,7 +51,7 @@ rule pe_remove_adapters_cutadapt:
"docker://zavolab/cutadapt:1.16"
threads: 8
log:
- os.path.join( config["local_log"], "paired_end", "{sample}", "remove_adapters_cutadapt.log")
+ os.path.join( config["log_dir"], "paired_end", "{sample}", "remove_adapters_cutadapt.log")
shell:
"(cutadapt \
-e 0.1 \
@@ -102,7 +102,7 @@ rule pe_remove_polya_cutadapt:
"docker://zavolab/cutadapt:1.16"
threads: 8
log:
- os.path.join( config["local_log"], "paired_end", "{sample}", "remove_polya_cutadapt.log")
+ os.path.join( config["log_dir"], "paired_end", "{sample}", "remove_polya_cutadapt.log")
shell:
'(cutadapt \
--match-read-wildcards \
@@ -181,7 +181,7 @@ rule pe_map_genome_star:
threads: 12
log:
- os.path.join( config["local_log"], "paired_end", "{sample}", "map_genome_star.log")
+ os.path.join( config["log_dir"], "paired_end", "{sample}", "map_genome_star.log")
shell:
"(STAR \
@@ -226,7 +226,7 @@ rule pe_index_genomic_alignment_samtools:
singularity:
"docker://zavolab/samtools:1.8"
log:
- os.path.join( config["local_log"], "paired_end", "{sample}", "index_genomic_alignment_samtools.log")
+ os.path.join( config["log_dir"], "paired_end", "{sample}", "index_genomic_alignment_samtools.log")
shell:
"(samtools index {input.bam} {output.bai};) &> {log}"
@@ -275,7 +275,7 @@ rule pe_quantification_salmon:
libType = lambda wildcards:
samples_table.loc[wildcards.sample, 'libtype']
log:
- os.path.join(config["local_log"], "paired_end", "{sample}", "genome_quantification_salmon.log")
+ os.path.join(config["log_dir"], "paired_end", "{sample}", "genome_quantification_salmon.log")
threads: 6
singularity:
"docker://zavolab/salmon:0.11.0"
@@ -330,7 +330,7 @@ rule pe_genome_quantification_kallisto:
"docker://zavolab/kallisto:0.46.1"
threads: 8
log:
- os.path.join(config["local_log"], "paired_end", "{sample}", "genome_quantification_kallisto.log")
+ os.path.join(config["log_dir"], "paired_end", "{sample}", "genome_quantification_kallisto.log")
shell:
"(kallisto quant \
-i {input.index} \
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index 0874686228ef9b603d02a808f20b1d5abc42fd96..08d4d228e8e18cf8e6c19208ccc87adaa7aa5610 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -10,7 +10,7 @@ rule fastqc:
singularity:
"docker://zavolab/fastqc:0.11.8"
log:
- os.path.join(config["local_log"], "single_end", "{sample}", "fastqc.log")
+ os.path.join(config["log_dir"], "single_end", "{sample}", "fastqc.log")
shell:
"(mkdir -p {output.outdir}; \
fastqc \
@@ -34,7 +34,7 @@ rule remove_adapters_cutadapt:
"docker://zavolab/cutadapt:1.16"
threads: 8
log:
- os.path.join(config["local_log"], "single_end", "{sample}", "remove_adapters_cutadapt.log")
+ os.path.join(config["log_dir"], "single_end", "{sample}", "remove_adapters_cutadapt.log")
shell:
"(cutadapt \
-e 0.1 \
@@ -61,7 +61,7 @@ rule remove_polya_cutadapt:
"docker://zavolab/cutadapt:1.16"
threads: 8
log:
- os.path.join(config["local_log"], "single_end", "{sample}", "remove_polya_cutadapt.log")
+ os.path.join(config["log_dir"], "single_end", "{sample}", "remove_polya_cutadapt.log")
shell:
"(cutadapt \
--match-read-wildcards \
@@ -117,7 +117,7 @@ rule map_genome_star:
"docker://zavolab/star:2.6.0a"
threads: 12
log:
- os.path.join(config["local_log"], "single_end", "{sample}", "map_genome_star.log")
+ os.path.join(config["log_dir"], "single_end", "{sample}", "map_genome_star.log")
shell:
"(STAR \
--runMode alignReads \
@@ -160,7 +160,7 @@ rule index_genomic_alignment_samtools:
"docker://zavolab/samtools:1.8"
threads: 1
log:
- os.path.join(config["local_log"], "single_end", "{sample}", "index_genomic_alignment_samtools.log")
+ os.path.join(config["log_dir"], "single_end", "{sample}", "index_genomic_alignment_samtools.log")
shell:
"(samtools index {input.bam} {output.bai};) &> {log}"
@@ -202,7 +202,7 @@ rule quantification_salmon:
libType = lambda wildcards:
samples_table.loc[wildcards.sample, "libtype"]
log:
- os.path.join(config["local_log"], "single_end", "{sample}", "quantification_salmon.log")
+ os.path.join(config["log_dir"], "single_end", "{sample}", "quantification_salmon.log")
threads: 12
singularity:
"docker://zavolab/salmon:0.11.0"
@@ -250,7 +250,7 @@ rule genome_quantification_kallisto:
directionality = lambda wildcards: samples_table.loc[wildcards.sample, 'kallisto_directionality']
threads: 8
log:
- os.path.join(config["local_log"],"kallisto_align_{sample}.log")
+ os.path.join(config["log_dir"],"kallisto_align_{sample}.log")
singularity:
"docker://zavolab/kallisto:0.46.1"
shell: