process BOWTIE2_BUILD { tag "$fasta" label 'process_high' conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' : 'quay.io/biocontainers/bowtie2:2.4.4--py36hd4290be_0' }" input: path fasta output: path 'bowtie2' , emit: index path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' """ mkdir bowtie2 bowtie2-build $args --threads $task.cpus $fasta bowtie2/${fasta.baseName} cat <<-END_VERSIONS > versions.yml "${task.process}": bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//') END_VERSIONS """ }