From 28a831bfacb47d84c2780d15977da8a306efabb7 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 29 Jan 2021 15:07:16 +0100
Subject: [PATCH] nf_modules: update output tuple to handle list as file_id
---
src/nf_modules/bedtools/main.nf | 4 ++--
src/nf_modules/bowtie2/main.nf | 14 +++++++-------
src/nf_modules/deeptools/main.nf | 7 ++++---
src/nf_modules/kallisto/main.nf | 4 ++--
src/nf_modules/macs2/main.nf | 6 +++---
src/nf_modules/sambamba/main.nf | 8 +++++---
6 files changed, 23 insertions(+), 20 deletions(-)
diff --git a/src/nf_modules/bedtools/main.nf b/src/nf_modules/bedtools/main.nf
index 4d3e4e1f..bd4a1890 100644
--- a/src/nf_modules/bedtools/main.nf
+++ b/src/nf_modules/bedtools/main.nf
@@ -12,7 +12,7 @@ process fasta_from_bed {
path bed
output:
- path "*_extracted.fasta", emit: fasta
+ tuple val(bed.baseName), path("*_extracted.fasta"), emit: fasta
script:
"""
@@ -50,7 +50,7 @@ process bam_to_fastq_pairedend {
tuple val(bam_id), path(bam)
output:
- tuple val(bam.baseName), path("*.fastq"), emit: fastq
+ tuple val(bam_id), path("*.fastq"), emit: fastq
script:
"""
diff --git a/src/nf_modules/bowtie2/main.nf b/src/nf_modules/bowtie2/main.nf
index e17e7f24..22465bae 100644
--- a/src/nf_modules/bowtie2/main.nf
+++ b/src/nf_modules/bowtie2/main.nf
@@ -78,8 +78,8 @@ process mapping_fastq_singleend {
tuple val(file_id), path(reads)
output:
- set file_id, "*.bam", emit: bam
- file "*_report.txt", emit: report
+ tuple val(file_id), path("*.bam"), emit: bam
+ path "*_report.txt", emit: report
script:
index_id = index[0]
@@ -93,13 +93,13 @@ bowtie2 --very-sensitive \
-p ${task.cpus} \
-x ${index_id} \
-U ${reads} 2> \
- ${file_id}_bowtie2_mapping_report_tmp.txt | \
- samtools view -Sb - > ${file_id}.bam
+ ${reads.baseName}_bowtie2_mapping_report_tmp.txt | \
+ samtools view -Sb - > ${reads.baseName}.bam
-if grep -q "Error" ${file_id}_bowtie2_mapping_report_tmp.txt; then
+if grep -q "Error" ${reads.baseName}_bowtie2_mapping_report_tmp.txt; then
exit 1
fi
-tail -n 19 ${file_id}_bowtie2_mapping_report_tmp.txt > \
- ${file_id}_bowtie2_mapping_report.txt
+tail -n 19 ${reads.baseName}_bowtie2_mapping_report_tmp.txt > \
+ ${reads.baseName}_bowtie2_mapping_report.txt
"""
}
diff --git a/src/nf_modules/deeptools/main.nf b/src/nf_modules/deeptools/main.nf
index ba2be7c5..3d012796 100644
--- a/src/nf_modules/deeptools/main.nf
+++ b/src/nf_modules/deeptools/main.nf
@@ -33,7 +33,8 @@ process bam_to_bigwig {
script:
"""
-bamCoverage -p ${task.cpus} --ignoreDuplicates -b ${bam} -o ${file_id}.bw
+bamCoverage -p ${task.cpus} --ignoreDuplicates -b ${bam} \
+ -o ${bam.simpleName}.bw
"""
}
@@ -57,7 +58,7 @@ computeMatrix scale-regions -S ${bw} \
-R ${bed} \
--beforeRegionStartLength 100 \
--afterRegionStartLength 100 \
- -o ${bed_file_id}.mat.gz
+ -o ${bed.simpleName}.mat.gz
"""
}
@@ -81,7 +82,7 @@ https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html
"""
plotProfile -m ${matrix} \
--plotFileFormat=pdf \
- -out ${file_id}.pdf \
+ -out ${matrix.simpleName}.pdf \
--plotType=fill \
--perGroup \
--plotTitle "${params.title}"
diff --git a/src/nf_modules/kallisto/main.nf b/src/nf_modules/kallisto/main.nf
index 5b0a150f..0517a1b5 100644
--- a/src/nf_modules/kallisto/main.nf
+++ b/src/nf_modules/kallisto/main.nf
@@ -57,7 +57,7 @@ process mapping_fastq_singleend {
tuple val(file_id), path(reads)
output:
- path "${pair_id}", emit: counts
+ tuple val(file_id), path("${pair_id}"), emit: counts
path "*_report.txt", emit: report
script:
@@ -66,6 +66,6 @@ mkdir ${file_id}
kallisto quant -i ${index} -t ${task.cpus} --single \
--bias --bootstrap-samples 100 -o ${file_id} \
-l ${params.mean} -s ${params.sd} \
-${reads} &> ${file_id}_kallisto_mapping_report.txt
+${reads} &> ${reads.simpleName}_kallisto_mapping_report.txt
"""
}
diff --git a/src/nf_modules/macs2/main.nf b/src/nf_modules/macs2/main.nf
index 9748cdc6..e30e0ee2 100644
--- a/src/nf_modules/macs2/main.nf
+++ b/src/nf_modules/macs2/main.nf
@@ -22,11 +22,11 @@ macs2 callpeak \
--call-summits "True"\
--control ${file_control} \
--keep-dup "auto" \
- --name ${file_id} \
+ --name ${bam_ip.simpleName} \
--gsize ${params.genome_size} 2> \
- ${file_ip}_macs2_report.txt
+ ${bam_ip.simpleName}_macs2_report.txt
-if grep -q "ERROR" ${file_ip}_macs2_report.txt; then
+if grep -q "ERROR" ${bam_ip.simpleName}_macs2_report.txt; then
echo "MACS2 error"
exit 1
fi
diff --git a/src/nf_modules/sambamba/main.nf b/src/nf_modules/sambamba/main.nf
index eb9bbb46..e07210bb 100644
--- a/src/nf_modules/sambamba/main.nf
+++ b/src/nf_modules/sambamba/main.nf
@@ -31,7 +31,7 @@ process sort_bam {
script:
"""
-sambamba sort -t ${task.cpus} -o ${file_id}_sorted.bam ${bam}
+sambamba sort -t ${task.cpus} -o ${bam.baseName}_sorted.bam ${bam}
"""
}
@@ -49,7 +49,9 @@ process split_bam {
tuple val(file_id), path("*_reverse.bam*"), emit: bam_reverse
script:
"""
-sambamba view -t ${task.cpus} -h -F "strand == '+'" ${bam} > ${file_id}_forward.bam
-sambamba view -t ${task.cpus} -h -F "strand == '-'" ${bam} > ${file_id}_reverse.bam
+sambamba view -t ${task.cpus} -h -F "strand == '+'" ${bam} > \
+ ${bam.baseName}_forward.bam
+sambamba view -t ${task.cpus} -h -F "strand == '-'" ${bam} > \
+ ${bam.baseName}_reverse.bam
"""
}
--
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