nf-core_modules/modules/bowtie2/align/main.nf
2022-05-13 15:26:41 +02:00

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process BOWTIE2_ALIGN {
tag "$meta.id"
label "process_high"
conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6" : null)
container "${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ?
"https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" :
"quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" }"
input:
tuple val(meta), path(reads)
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
"""
}