mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
Merge pull request #1645 from matthdsm/update/bowtie2-align
bowtie2: remove code duplication
This commit is contained in:
Matthias De Smet
GitHub
commit
1dccf12077
2 changed files with 62 additions and 133 deletions
|
|
@ -1,11 +1,11 @@
|
||||||
process BOWTIE2_ALIGN {
|
process BOWTIE2_ALIGN {
|
||||||
tag "$meta.id"
|
tag "$meta.id"
|
||||||
label 'process_high'
|
label "process_high"
|
||||||
|
|
||||||
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6' : null)
|
conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6" : null)
|
||||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
container "${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ?
|
||||||
'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' :
|
"https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" :
|
||||||
'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' }"
|
"quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" }"
|
||||||
|
|
||||||
input:
|
input:
|
||||||
tuple val(meta), path(reads)
|
tuple val(meta), path(reads)
|
||||||
|
|
@ -13,59 +13,50 @@ process BOWTIE2_ALIGN {
|
||||||
val save_unaligned
|
val save_unaligned
|
||||||
|
|
||||||
output:
|
output:
|
||||||
tuple val(meta), path('*.bam') , emit: bam
|
tuple val(meta), path("*.bam") , emit: bam
|
||||||
tuple val(meta), path('*.log') , emit: log
|
tuple val(meta), path("*.log") , emit: log
|
||||||
tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true
|
tuple val(meta), path("*fastq.gz"), emit: fastq, optional:true
|
||||||
path "versions.yml" , emit: versions
|
path "versions.yml" , emit: versions
|
||||||
|
|
||||||
when:
|
when:
|
||||||
task.ext.when == null || task.ext.when
|
task.ext.when == null || task.ext.when
|
||||||
|
|
||||||
script:
|
script:
|
||||||
def args = task.ext.args ?: ''
|
def args = task.ext.args ?: ""
|
||||||
def args2 = task.ext.args2 ?: ''
|
def args2 = task.ext.args2 ?: ""
|
||||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||||
if (meta.single_end) {
|
|
||||||
def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
|
|
||||||
"""
|
|
||||||
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
|
|
||||||
[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
|
|
||||||
[ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
|
|
||||||
bowtie2 \\
|
|
||||||
-x \$INDEX \\
|
|
||||||
-U $reads \\
|
|
||||||
--threads $task.cpus \\
|
|
||||||
$unaligned \\
|
|
||||||
$args \\
|
|
||||||
2> ${prefix}.bowtie2.log \\
|
|
||||||
| samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
|
|
||||||
|
|
||||||
cat <<-END_VERSIONS > versions.yml
|
def unaligned = ""
|
||||||
"${task.process}":
|
def reads_args = ""
|
||||||
bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
|
if (meta.single_end) {
|
||||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ""
|
||||||
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
|
reads_args = "-U ${reads}"
|
||||||
END_VERSIONS
|
|
||||||
"""
|
|
||||||
} else {
|
} else {
|
||||||
def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
|
unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ""
|
||||||
|
reads_args = "-1 ${reads[0]} -2 ${reads[1]}"
|
||||||
|
}
|
||||||
|
|
||||||
|
def samtools_command = "samtools view -@ $task.cpus --bam --with-header ${args2} > ${prefix}.bam"
|
||||||
|
|
||||||
|
|
||||||
"""
|
"""
|
||||||
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
|
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/.rev.1.bt2//"`
|
||||||
[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
|
[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/.rev.1.bt2l//"`
|
||||||
[ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
|
[ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
|
||||||
|
|
||||||
bowtie2 \\
|
bowtie2 \\
|
||||||
-x \$INDEX \\
|
-x \$INDEX \\
|
||||||
-1 ${reads[0]} \\
|
$reads_args \\
|
||||||
-2 ${reads[1]} \\
|
|
||||||
--threads $task.cpus \\
|
--threads $task.cpus \\
|
||||||
$unaligned \\
|
$unaligned \\
|
||||||
$args \\
|
$args \\
|
||||||
2> ${prefix}.bowtie2.log \\
|
2> ${prefix}.bowtie2.log \\
|
||||||
| samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
|
| $samtools_command
|
||||||
|
|
||||||
if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
|
if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
|
||||||
mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
|
mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
|
||||||
fi
|
fi
|
||||||
|
|
||||||
if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
|
if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
|
||||||
mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
|
mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
|
||||||
fi
|
fi
|
||||||
|
|
@ -78,4 +69,4 @@ process BOWTIE2_ALIGN {
|
||||||
END_VERSIONS
|
END_VERSIONS
|
||||||
"""
|
"""
|
||||||
}
|
}
|
||||||
}
|
|
||||||
|
|
|
||||||
|
|
@ -1,83 +1,21 @@
|
||||||
- name: bowtie2 align single-end
|
- name: bowtie2 align test_bowtie2_align_single_end
|
||||||
command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
|
command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
|
||||||
tags:
|
tags:
|
||||||
- bowtie2
|
|
||||||
- bowtie2/align
|
- bowtie2/align
|
||||||
|
- bowtie2
|
||||||
files:
|
files:
|
||||||
- path: ./output/bowtie2/test.bam
|
- path: output/bowtie2/test.bam
|
||||||
- path: ./output/bowtie2/test.bowtie2.log
|
- path: output/bowtie2/test.bowtie2.log
|
||||||
- path: ./output/bowtie2/bowtie2/genome.3.bt2
|
md5sum: 7b8a9e61b7646da1089b041333c41a87
|
||||||
md5sum: 4ed93abba181d8dfab2e303e33114777
|
- path: output/bowtie2/versions.yml
|
||||||
- path: ./output/bowtie2/bowtie2/genome.2.bt2
|
|
||||||
md5sum: 47b153cd1319abc88dda532462651fcf
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.1.bt2
|
|
||||||
md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.4.bt2
|
|
||||||
md5sum: c25be5f8b0378abf7a58c8a880b87626
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.rev.1.bt2
|
|
||||||
md5sum: 52be6950579598a990570fbcf5372184
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
|
|
||||||
md5sum: e3b4ef343dea4dd571642010a7d09597
|
|
||||||
|
|
||||||
- name: bowtie2 align paired-end
|
- name: bowtie2 align test_bowtie2_align_paired_end
|
||||||
command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
|
command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
|
||||||
tags:
|
tags:
|
||||||
- bowtie2
|
|
||||||
- bowtie2/align
|
- bowtie2/align
|
||||||
files:
|
|
||||||
- path: ./output/bowtie2/test.bam
|
|
||||||
- path: ./output/bowtie2/test.bowtie2.log
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.3.bt2
|
|
||||||
md5sum: 4ed93abba181d8dfab2e303e33114777
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.2.bt2
|
|
||||||
md5sum: 47b153cd1319abc88dda532462651fcf
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.1.bt2
|
|
||||||
md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.4.bt2
|
|
||||||
md5sum: c25be5f8b0378abf7a58c8a880b87626
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.rev.1.bt2
|
|
||||||
md5sum: 52be6950579598a990570fbcf5372184
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
|
|
||||||
md5sum: e3b4ef343dea4dd571642010a7d09597
|
|
||||||
|
|
||||||
- name: bowtie2 align single-end large-index
|
|
||||||
command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config --force_large_index
|
|
||||||
tags:
|
|
||||||
- bowtie2
|
- bowtie2
|
||||||
- bowtie2/align
|
|
||||||
files:
|
files:
|
||||||
- path: ./output/bowtie2/test.bam
|
- path: output/bowtie2/test.bam
|
||||||
- path: ./output/bowtie2/test.bowtie2.log
|
- path: output/bowtie2/test.bowtie2.log
|
||||||
- path: ./output/bowtie2/bowtie2/genome.3.bt2l
|
md5sum: bd89ce1b28c93bf822bae391ffcedd19
|
||||||
md5sum: 8952b3e0b1ce9a7a5916f2e147180853
|
- path: output/bowtie2/versions.yml
|
||||||
- path: ./output/bowtie2/bowtie2/genome.2.bt2l
|
|
||||||
md5sum: 22c284084784a0720989595e0c9461fd
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.1.bt2l
|
|
||||||
md5sum: 07d811cd4e350d56267183d2ac7023a5
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.4.bt2l
|
|
||||||
md5sum: c25be5f8b0378abf7a58c8a880b87626
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.rev.1.bt2l
|
|
||||||
md5sum: fda48e35925fb24d1c0785f021981e25
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.rev.2.bt2l
|
|
||||||
md5sum: 802c26d32b970e1b105032b7ce7348b4
|
|
||||||
|
|
||||||
- name: bowtie2 align paired-end large-index
|
|
||||||
command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config --force_large_index
|
|
||||||
tags:
|
|
||||||
- bowtie2
|
|
||||||
- bowtie2/align
|
|
||||||
files:
|
|
||||||
- path: ./output/bowtie2/test.bam
|
|
||||||
- path: ./output/bowtie2/test.bowtie2.log
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.3.bt2l
|
|
||||||
md5sum: 8952b3e0b1ce9a7a5916f2e147180853
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.2.bt2l
|
|
||||||
md5sum: 22c284084784a0720989595e0c9461fd
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.1.bt2l
|
|
||||||
md5sum: 07d811cd4e350d56267183d2ac7023a5
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.4.bt2l
|
|
||||||
md5sum: c25be5f8b0378abf7a58c8a880b87626
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.rev.1.bt2l
|
|
||||||
md5sum: fda48e35925fb24d1c0785f021981e25
|
|
||||||
- path: ./output/bowtie2/bowtie2/genome.rev.2.bt2l
|
|
||||||
md5sum: 802c26d32b970e1b105032b7ce7348b4
|
|
||||||
|
|
|
||||||
Loading…
Reference in a new issue