process BOWTIE2_ALIGN { tag "$meta.id" label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.14 conda-forge::pigz=2.6' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' : 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' }" input: tuple val(meta), path(reads) path index val save_unaligned 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 script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' 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//'` bowtie2 \\ -x \$INDEX \\ -U $reads \\ --threads $task.cpus \\ $unaligned \\ $args \\ 2> ${prefix}.bowtie2.log \\ | samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam - cat <<-END_VERSIONS > versions.yml "${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 """ } else { def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' """ INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'` bowtie2 \\ -x \$INDEX \\ -1 ${reads[0]} \\ -2 ${reads[1]} \\ --threads $task.cpus \\ $unaligned \\ $args \\ 2> ${prefix}.bowtie2.log \\ | samtools view -@ $task.cpus $args2 -bhS -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 """ } }