From fd494cd58ab7a994d75e34fdc2477b24d239b155 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 14 Apr 2021 18:20:26 +0200
Subject: [PATCH] bowtie2: update to match contributing.md
---
src/nf_modules/bowtie2/main.nf | 155 ++++++++++-----------------------
1 file changed, 47 insertions(+), 108 deletions(-)
diff --git a/src/nf_modules/bowtie2/main.nf b/src/nf_modules/bowtie2/main.nf
index a626d4f3..b9053c71 100644
--- a/src/nf_modules/bowtie2/main.nf
+++ b/src/nf_modules/bowtie2/main.nf
@@ -2,17 +2,21 @@ version = "2.3.4.1"
container_url = "lbmc/bowtie2:${version}"
params.index_fasta = ""
+params.index_fasta_out = ""
process index_fasta {
container = "${container_url}"
label "big_mem_multi_cpus"
- tag "$fasta.baseName"
+ tag "$file_id"
+ if (params.index_fasta_out != "") {
+ publishDir "results/${params.index_fasta_out}", mode: 'copy'
+ }
input:
- path fasta
+ tuple val(file_id), path(fasta)
output:
- path "*.index*", emit: index
- path "*_report.txt", emit: report
+ tuple val(file_id), path("*.index*"), emit: index
+ tuple val(file_id), path("*_report.txt"), emit: report
script:
"""
@@ -28,64 +32,14 @@ fi
}
params.mapping_fastq = "--very-sensitive"
+params.mapping_fastq_out = ""
process mapping_fastq {
container = "${container_url}"
label "big_mem_multi_cpus"
- tag "$pair_id"
-
- input:
- path index
- tuple val(pair_id), path(reads)
-
- output:
- tuple val(pair_id), path("*.bam"), emit: bam
- path "*_report.txt", emit: report
-
- script:
- index_id = index[0]
- for (index_file in index) {
- if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
- index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
- }
+ tag "$file_id"
+ if (params.mapping_fastq_out != "") {
+ publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
}
-if (reads instanceof List)
-"""
-bowtie2 ${params.mapping_fastq} \
- -p ${task.cpus} \
- -x ${index_id} \
- -1 ${reads[0]} \
- -2 ${reads[1]} 2> \
- ${pair_id}_bowtie2_mapping_report_tmp.txt | \
- samtools view -Sb - > ${pair_id}.bam
-
-if grep -q "Error" ${pair_id}_bowtie2_mapping_report_tmp.txt; then
- exit 1
-fi
-tail -n 19 ${pair_id}_bowtie2_mapping_report_tmp.txt > \
- ${pair_id}_bowtie2_mapping_report.txt
-"""
-else
-"""
-bowtie2 ${params.mapping_fastq} \
- -p ${task.cpus} \
- -x ${index_id} \
- -U ${reads} 2> \
- ${reads.baseName}_bowtie2_mapping_report_tmp.txt | \
- samtools view -Sb - > ${reads.baseName}.bam
-
-if grep -q "Error" ${reads.baseName}_bowtie2_mapping_report_tmp.txt; then
- exit 1
-fi
-tail -n 19 ${reads.baseName}_bowtie2_mapping_report_tmp.txt > \
- ${reads.baseName}_bowtie2_mapping_report.txt
-"""
-}
-
-params.mapping_fastq_pairedend = "--very-sensitive"
-process mapping_fastq_pairedend {
- container = "${container_url}"
- label "big_mem_multi_cpus"
- tag "$pair_id"
input:
path index
@@ -102,56 +56,41 @@ process mapping_fastq_pairedend {
index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
}
}
-"""
-bowtie2 ${params.mapping_fastq_pairedend} \
- -p ${task.cpus} \
- -x ${index_id} \
- -1 ${reads[0]} \
- -2 ${reads[1]} 2> \
- ${pair_id}_bowtie2_mapping_report_tmp.txt | \
- samtools view -Sb - > ${pair_id}.bam
-
-if grep -q "Error" ${pair_id}_bowtie2_mapping_report_tmp.txt; then
- exit 1
-fi
-tail -n 19 ${pair_id}_bowtie2_mapping_report_tmp.txt > \
- ${pair_id}_bowtie2_mapping_report.txt
-"""
-}
-
-params.mapping_fastq_singleend = "--very-sensitive"
-process mapping_fastq_singleend {
- container = "${container_url}"
- label "big_mem_multi_cpus"
- tag "$file_id"
-
- input:
- path index
- tuple val(file_id), path(reads)
-
- output:
- tuple val(file_id), path("*.bam"), emit: bam
- path "*_report.txt", emit: report
-
- script:
- index_id = index[0]
- for (index_file in index) {
- if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
- index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
- }
+ if (file_id instanceof List){
+ file_prefix = file_id[0]
+ } else {
+ file_prefix = file_id
}
-"""
-bowtie2 ${params.mapping_fastq_singleend} \
- -p ${task.cpus} \
- -x ${index_id} \
- -U ${reads} 2> \
- ${reads.baseName}_bowtie2_mapping_report_tmp.txt | \
- samtools view -Sb - > ${reads.baseName}.bam
-if grep -q "Error" ${reads.baseName}_bowtie2_mapping_report_tmp.txt; then
- exit 1
-fi
-tail -n 19 ${reads.baseName}_bowtie2_mapping_report_tmp.txt > \
- ${reads.baseName}_bowtie2_mapping_report.txt
-"""
+ if (reads.size() == 2)
+ """
+ bowtie2 ${params.mapping_fastq} \
+ -p ${task.cpus} \
+ -x ${index_id} \
+ -1 ${reads[0]} \
+ -2 ${reads[1]} 2> \
+ ${file_prefix}_bowtie2_mapping_report_tmp.txt | \
+ samtools view -Sb - > ${file_prefix}.bam
+
+ if grep -q "Error" ${file_prefix}_bowtie2_mapping_report_tmp.txt; then
+ exit 1
+ fi
+ tail -n 19 ${file_prefix}_bowtie2_mapping_report_tmp.txt > \
+ ${file_prefix}_bowtie2_mapping_report.txt
+ """
+ else if (reads.size() == 1)
+ """
+ bowtie2 ${params.mapping_fastq} \
+ -p ${task.cpus} \
+ -x ${index_id} \
+ -U ${reads} 2> \
+ ${file_prefix}_bowtie2_mapping_report_tmp.txt | \
+ samtools view -Sb - > ${file_prefix}.bam
+
+ if grep -q "Error" ${file_prefix}_bowtie2_mapping_report_tmp.txt; then
+ exit 1
+ fi
+ tail -n 19 ${file_prefix}_bowtie2_mapping_report_tmp.txt > \
+ ${file_prefix}_bowtie2_mapping_report.txt
+ """
}
--
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