From 5236de956b02782c1eafd17d7c52581f6f7b4a3d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 7 Jun 2018 10:02:32 +0200
Subject: [PATCH] paired.nf files : pass the pair_id information in output
---
src/nf_modules/BEDtools/bedtools.nf | 5 +++--
src/nf_modules/Bowtie2/bowtie2.nf | 2 +-
src/nf_modules/Bowtie2/tests/mapping_paired.nf | 3 ++-
src/nf_modules/Kallisto/kallisto.nf | 6 +++---
src/nf_modules/Kallisto/tests/mapping_paired.nf | 4 ++--
src/nf_modules/UrQt/tests/trimming_paired.nf | 6 ++++--
src/nf_modules/UrQt/urqt.nf | 8 ++++----
src/nf_modules/cutadapt/cutadapt.nf | 4 ++--
src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf | 4 ++--
src/nf_modules/cutadapt/tests/trimming_paired.nf | 4 ++--
10 files changed, 25 insertions(+), 21 deletions(-)
diff --git a/src/nf_modules/BEDtools/bedtools.nf b/src/nf_modules/BEDtools/bedtools.nf
index 6d6bf089..297fd9ef 100644
--- a/src/nf_modules/BEDtools/bedtools.nf
+++ b/src/nf_modules/BEDtools/bedtools.nf
@@ -1,7 +1,8 @@
/*
* bedtools :
-* Imputs : fastq files
-* Output : fastq files
+* Imputs : fasta files
+* Imputs : bed files
+* Output : fasta files
*/
/* fasta extraction */
diff --git a/src/nf_modules/Bowtie2/bowtie2.nf b/src/nf_modules/Bowtie2/bowtie2.nf
index 095d85ff..30b75312 100644
--- a/src/nf_modules/Bowtie2/bowtie2.nf
+++ b/src/nf_modules/Bowtie2/bowtie2.nf
@@ -66,7 +66,7 @@ process mapping_fastq {
file index from index_files.toList()
output:
- file "*.bam" into bam_files
+ set pair_id, "*.bam" into bam_files
script:
"""
diff --git a/src/nf_modules/Bowtie2/tests/mapping_paired.nf b/src/nf_modules/Bowtie2/tests/mapping_paired.nf
index 048db49b..835d0ca3 100644
--- a/src/nf_modules/Bowtie2/tests/mapping_paired.nf
+++ b/src/nf_modules/Bowtie2/tests/mapping_paired.nf
@@ -23,7 +23,7 @@ process mapping_fastq {
file index from index_files.toList()
output:
- file "*.bam" into bam_files
+ set pair_id, "*.bam" into bam_files
script:
"""
@@ -37,3 +37,4 @@ if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
fi
"""
}
+
diff --git a/src/nf_modules/Kallisto/kallisto.nf b/src/nf_modules/Kallisto/kallisto.nf
index 1f21a1fa..8867a0c3 100644
--- a/src/nf_modules/Kallisto/kallisto.nf
+++ b/src/nf_modules/Kallisto/kallisto.nf
@@ -58,7 +58,7 @@ process mapping_fastq {
publishDir "results/mapping/quantification/", mode: 'copy'
input:
- file reads from fastq_files
+ set pair_id, file(reads) from fastq_files
file index from index_files.toList()
output:
@@ -68,8 +68,8 @@ process mapping_fastq {
"""
mkdir ${reads[0].baseName}
kallisto quant -i ${index} -t ${task.cpus} \
---bias --bootstrap-samples 100 -o ${reads[0].baseName} \
-${reads[0]} ${reads[1]} &> ${reads[0].baseName}_kallisto_report.txt
+--bias --bootstrap-samples 100 -o ${pair_id} \
+${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_report.txt
"""
}
diff --git a/src/nf_modules/Kallisto/tests/mapping_paired.nf b/src/nf_modules/Kallisto/tests/mapping_paired.nf
index 71b9f471..8e8f94c9 100644
--- a/src/nf_modules/Kallisto/tests/mapping_paired.nf
+++ b/src/nf_modules/Kallisto/tests/mapping_paired.nf
@@ -14,7 +14,7 @@ Channel
.set { index_files }
process mapping_fastq {
- tag "$pair_id"
+ tag "$reads"
cpus 4
publishDir "results/mapping/quantification/", mode: 'copy'
@@ -27,7 +27,7 @@ process mapping_fastq {
script:
"""
-mkdir ${pair_id}
+mkdir ${reads[0].baseName}
kallisto quant -i ${index} -t ${task.cpus} \
--bias --bootstrap-samples 100 -o ${pair_id} \
${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_report.txt
diff --git a/src/nf_modules/UrQt/tests/trimming_paired.nf b/src/nf_modules/UrQt/tests/trimming_paired.nf
index 4c289c0e..7720b12f 100644
--- a/src/nf_modules/UrQt/tests/trimming_paired.nf
+++ b/src/nf_modules/UrQt/tests/trimming_paired.nf
@@ -6,14 +6,15 @@ Channel
.set { fastq_files }
process trimming {
- tag "$pair_id"
+ tag "${reads}"
cpus 4
+ publishDir "results/fastq/trimming/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
output:
- file "*_trim_R{1,2}.fastq.gz" into fastq_files_cut
+ set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
script:
"""
@@ -23,3 +24,4 @@ UrQt --t 20 --m ${task.cpus} --gz \
> ${pair_id}_trimming_report.txt
"""
}
+
diff --git a/src/nf_modules/UrQt/urqt.nf b/src/nf_modules/UrQt/urqt.nf
index 165af95d..d2403363 100644
--- a/src/nf_modules/UrQt/urqt.nf
+++ b/src/nf_modules/UrQt/urqt.nf
@@ -24,17 +24,17 @@ process trimming {
publishDir "results/fastq/trimming/", mode: 'copy'
input:
- file reads from fastq_files
+ set pair_id, file(reads) from fastq_files
output:
- file "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
+ set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
script:
"""
UrQt --t 20 --m ${task.cpus} --gz \
--in ${reads[0]} --inpair ${reads[1]} \
---out ${reads[0].baseName}_trim_R1.fastq.gz --outpair ${reads[1].baseName}_trim_R2.fastq.gz \
-> ${reads[0].baseName}_trimming_report.txt
+--out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
+> ${pair_id}_trimming_report.txt
"""
}
diff --git a/src/nf_modules/cutadapt/cutadapt.nf b/src/nf_modules/cutadapt/cutadapt.nf
index e2a0681a..204a9e5a 100644
--- a/src/nf_modules/cutadapt/cutadapt.nf
+++ b/src/nf_modules/cutadapt/cutadapt.nf
@@ -27,7 +27,7 @@ process adaptor_removal {
set pair_id, file(reads) from fastq_files
output:
- file "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
+ set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
script:
"""
@@ -91,7 +91,7 @@ process trimming {
set pair_id, file(reads) from fastq_files
output:
- file "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
+ set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
script:
"""
diff --git a/src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf b/src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf
index d665d236..f78d5c2d 100644
--- a/src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf
+++ b/src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf
@@ -7,12 +7,13 @@ Channel
process adaptor_removal {
tag "$pair_id"
+ publishDir "results/fastq/adaptor_removal/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
output:
- file "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
+ set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
script:
"""
@@ -21,4 +22,3 @@ process adaptor_removal {
${reads[0]} ${reads[1]} > ${pair_id}_report.txt
"""
}
-
diff --git a/src/nf_modules/cutadapt/tests/trimming_paired.nf b/src/nf_modules/cutadapt/tests/trimming_paired.nf
index d0b83e1c..704240f4 100644
--- a/src/nf_modules/cutadapt/tests/trimming_paired.nf
+++ b/src/nf_modules/cutadapt/tests/trimming_paired.nf
@@ -7,12 +7,13 @@ Channel
process trimming {
tag "$pair_id"
+ publishDir "results/fastq/trimming/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
output:
- file "*_trim_R{1,2}.fastq.gz" into fastq_files_cut
+ set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
script:
"""
@@ -21,4 +22,3 @@ process trimming {
${reads[0]} ${reads[1]} > ${pair_id}_report.txt
"""
}
-
--
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