kkonganti@0: process SAMTOOLS_FASTQ {
kkonganti@0:     tag "$meta.id"
kkonganti@0:     label 'process_micro'
kkonganti@0: 
kkonganti@0:     module (params.enable_module ? "${params.swmodulepath}${params.fs}samtools${params.fs}1.13" : null)
kkonganti@0:     conda (params.enable_conda ? "bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::bzip2" : null)
kkonganti@0:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@0:         'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' :
kkonganti@0:         'quay.io/biocontainers/samtools:1.18--h50ea8bc_1' }"
kkonganti@0: 
kkonganti@0:     input:
kkonganti@0:         tuple val(meta), path(input)
kkonganti@0:         val(interleave)
kkonganti@0: 
kkonganti@0:     output:
kkonganti@0:         tuple val(meta), path("*_{1,2}.fastq.gz")      , optional:true, emit: fastq
kkonganti@0:         tuple val(meta), path("*_{1,2}.fastq.gz")      , optional:true, emit: mapped_refs
kkonganti@0:         tuple val(meta), path("*_interleaved.fastq")   , optional:true, emit: interleaved
kkonganti@0:         tuple val(meta), path("*_singleton.fastq.gz")  , optional:true, emit: singleton
kkonganti@0:         tuple val(meta), path("*_other.fastq.gz")      , optional:true, emit: other
kkonganti@0:         path  "versions.yml"                           , emit: versions
kkonganti@0: 
kkonganti@0:     when:
kkonganti@0:         task.ext.when == null || task.ext.when
kkonganti@0: 
kkonganti@0:     script:
kkonganti@0:         def args = task.ext.args ?: ''
kkonganti@0:         def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@0:         def output = ( interleave && ! meta.single_end ) ? "> ${prefix}_interleaved.fastq" :
kkonganti@0:             meta.single_end ? "-1 ${prefix}_1.fastq.gz -s ${prefix}_singleton.fastq.gz" :
kkonganti@0:             "-1 ${prefix}_1.fastq.gz -2 ${prefix}_2.fastq.gz -s ${prefix}_singleton.fastq.gz"
kkonganti@0:         """
kkonganti@0:         samtools \\
kkonganti@0:             fastq \\
kkonganti@0:             $args \\
kkonganti@0:             --threads ${task.cpus-1} \\
kkonganti@0:             -0 ${prefix}_other.fastq.gz \\
kkonganti@0:             $input \\
kkonganti@0:             $output
kkonganti@0: 
kkonganti@0:         samtools \\
kkonganti@0:             view \\
kkonganti@0:             $args2 \\
kkonganti@0:             --threads ${task.cpus-1} \\
kkonganti@0:             $input \\
kkonganti@0:             | grep -v '*' | cut -f3 | sort -u > mapped_refs.txt
kkonganti@0: 
kkonganti@0:         cat <<-END_VERSIONS > versions.yml
kkonganti@0:         "${task.process}":
kkonganti@0:             samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
kkonganti@0:         END_VERSIONS
kkonganti@0:         """
kkonganti@0: }