kkonganti@105: process SEQTK_SEQ {
kkonganti@105:     tag "$meta.id"
kkonganti@105:     label 'process_mem_low'
kkonganti@105: 
kkonganti@105:     module (params.enable_module ? "${params.swmodulepath}${params.fs}seqtk${params.fs}1.3-r106" : null)
kkonganti@105:     conda (params.enable_conda ? "bioconda::seqtk=1.3 conda-forge::gzip" : null)
kkonganti@105:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@105:         'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' :
kkonganti@105:         'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }"
kkonganti@105: 
kkonganti@105:     input:
kkonganti@105:     tuple val(meta), path(fastx)
kkonganti@105: 
kkonganti@105:     output:
kkonganti@105:     tuple val(meta), path("*.gz"), emit: fastx
kkonganti@105:     path "versions.yml"          , emit: versions
kkonganti@105: 
kkonganti@105:     when:
kkonganti@105:     task.ext.when == null || task.ext.when
kkonganti@105: 
kkonganti@105:     script:
kkonganti@105:     def args = task.ext.args ?: ''
kkonganti@105:     def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@105: 
kkonganti@105:     def extension = "fastq"
kkonganti@105:     if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/ || "$args" ==~ /\-[aA]/ ) {
kkonganti@105:         extension = "fasta"
kkonganti@105:     }
kkonganti@105:     """
kkonganti@105:     seqtk \\
kkonganti@105:         seq \\
kkonganti@105:         $args \\
kkonganti@105:         $fastx | \\
kkonganti@105:         gzip -c > ${prefix}.seqtk-seq.${task.index}.${extension}.gz
kkonganti@105: 
kkonganti@105:     cat <<-END_VERSIONS > versions.yml
kkonganti@105:     "${task.process}":
kkonganti@105:         seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
kkonganti@105:         gzip: \$( echo \$(gzip --version 2>&1) | sed 's/^.*(gzip) //; s/gzip //; s/ Copyright.*\$//' )
kkonganti@105:     END_VERSIONS
kkonganti@105:     """
kkonganti@105: }