You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
72 lines
2.5 KiB
Plaintext
72 lines
2.5 KiB
Plaintext
process BOWTIE2_ALIGN {
|
|
tag "$meta.id"
|
|
label "process_high"
|
|
|
|
conda "bioconda::bowtie2=2.4.4 bioconda::samtools=1.16.1 conda-forge::pigz=2.6"
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' :
|
|
'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }"
|
|
|
|
input:
|
|
tuple val(meta) , path(reads)
|
|
tuple val(meta2), path(index)
|
|
val save_unaligned
|
|
val sort_bam
|
|
|
|
output:
|
|
tuple val(meta), path("*.bam") , emit: bam
|
|
tuple val(meta), path("*.log") , emit: log
|
|
tuple val(meta), path("*fastq.gz"), emit: fastq, optional:true
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ""
|
|
def args2 = task.ext.args2 ?: ""
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
|
|
def unaligned = ""
|
|
def reads_args = ""
|
|
if (meta.single_end) {
|
|
unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ""
|
|
reads_args = "-U ${reads}"
|
|
} else {
|
|
unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ""
|
|
reads_args = "-1 ${reads[0]} -2 ${reads[1]}"
|
|
}
|
|
|
|
def samtools_command = sort_bam ? 'sort' : 'view'
|
|
|
|
"""
|
|
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 "Bowtie2 index files not found" 1>&2 && exit 1
|
|
|
|
bowtie2 \\
|
|
-x \$INDEX \\
|
|
$reads_args \\
|
|
--threads $task.cpus \\
|
|
$unaligned \\
|
|
$args \\
|
|
2> ${prefix}.bowtie2.log \\
|
|
| samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
|
|
|
|
if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
|
|
mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
|
|
fi
|
|
|
|
if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
|
|
mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
|
|
fi
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
|
|
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
|
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|