kkonganti@17: process FASTP {
kkonganti@17:     tag "$meta.id"
kkonganti@17:     label 'process_low'
kkonganti@17: 
kkonganti@17:     module (params.enable_module ? "${params.swmodulepath}${params.fs}fastp${params.fs}0.23.2" : null)
kkonganti@17:     conda (params.enable_conda ? "bioconda::fastp=0.23.2 conda-forge::isa-l" : null)
kkonganti@17:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@17:         'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' :
kkonganti@17:         'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }"
kkonganti@17: 
kkonganti@17:     input:
kkonganti@17:         tuple val(meta), path(reads)
kkonganti@17: 
kkonganti@17:     output:
kkonganti@17:         tuple val(meta), path('*.fastp.fastq.gz') , emit: passed_reads, optional: true
kkonganti@17:         tuple val(meta), path('*.fail.fastq.gz')  , emit: failed_reads, optional: true
kkonganti@17:         tuple val(meta), path('*.merged.fastq.gz'), emit: merged_reads, optional: true
kkonganti@17:         tuple val(meta), path('*.json')           , emit: json
kkonganti@17:         tuple val(meta), path('*.html')           , emit: html
kkonganti@17:         tuple val(meta), path('*.log')            , emit: log
kkonganti@17:         path "versions.yml"                       , emit: versions
kkonganti@17: 
kkonganti@17:     when:
kkonganti@17:         task.ext.when == null || task.ext.when
kkonganti@17: 
kkonganti@17:     script:
kkonganti@17:         def args = task.ext.args ?: ''
kkonganti@17:         def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@17:         def fail_fastq = params.fastp_failed_out && meta.single_end ? "--failed_out ${prefix}.fail.fastq.gz" : params.fastp_failed_out && !meta.single_end ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
kkonganti@17:         // Added soft-links to original fastqs for consistent naming in MultiQC
kkonganti@17:         // Use single ended for interleaved. Add --interleaved_in in config.
kkonganti@17:         if ( task.ext.args?.contains('--interleaved_in') ) {
kkonganti@17:             """
kkonganti@17:             [ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
kkonganti@17: 
kkonganti@17:             fastp \\
kkonganti@17:                 --stdout \\
kkonganti@17:                 --in1 ${prefix}.fastq.gz \\
kkonganti@17:                 --thread $task.cpus \\
kkonganti@17:                 --json ${prefix}.fastp.json \\
kkonganti@17:                 --html ${prefix}.fastp.html \\
kkonganti@17:                 $fail_fastq \\
kkonganti@17:                 $args \\
kkonganti@17:                 2> ${prefix}.fastp.log \\
kkonganti@17:             | gzip -c > ${prefix}.fastp.fastq.gz
kkonganti@17: 
kkonganti@17:             cat <<-END_VERSIONS > versions.yml
kkonganti@17:             "${task.process}":
kkonganti@17:                 fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
kkonganti@17:             END_VERSIONS
kkonganti@17:             """
kkonganti@17:         } else if (meta.single_end) {
kkonganti@17:             """
kkonganti@17:             [ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
kkonganti@17: 
kkonganti@17:             fastp \\
kkonganti@17:                 --in1 ${prefix}.fastq.gz \\
kkonganti@17:                 --out1  ${prefix}.fastp.fastq.gz \\
kkonganti@17:                 --thread $task.cpus \\
kkonganti@17:                 --json ${prefix}.fastp.json \\
kkonganti@17:                 --html ${prefix}.fastp.html \\
kkonganti@17:                 $fail_fastq \\
kkonganti@17:                 $args \\
kkonganti@17:                 2> ${prefix}.fastp.log
kkonganti@17: 
kkonganti@17:             cat <<-END_VERSIONS > versions.yml
kkonganti@17:             "${task.process}":
kkonganti@17:                 fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
kkonganti@17:             END_VERSIONS
kkonganti@17:             """
kkonganti@17:         } else {
kkonganti@17:             def merge_fastq = params.fastp_merged_out ? "-m --merged_out ${prefix}.merged.fastq.gz" : ''
kkonganti@17:             """
kkonganti@17:             [ ! -f  ${prefix}_1.fastq.gz ] && ln -sf ${reads[0]} ${prefix}_1.fastq.gz
kkonganti@17:             [ ! -f  ${prefix}_2.fastq.gz ] && ln -sf ${reads[1]} ${prefix}_2.fastq.gz
kkonganti@17:             fastp \\
kkonganti@17:                 --in1 ${prefix}_1.fastq.gz \\
kkonganti@17:                 --in2 ${prefix}_2.fastq.gz \\
kkonganti@17:                 --out1 ${prefix}_1.fastp.fastq.gz \\
kkonganti@17:                 --out2 ${prefix}_2.fastp.fastq.gz \\
kkonganti@17:                 --json ${prefix}.fastp.json \\
kkonganti@17:                 --html ${prefix}.fastp.html \\
kkonganti@17:                 $fail_fastq \\
kkonganti@17:                 $merge_fastq \\
kkonganti@17:                 --thread $task.cpus \\
kkonganti@17:                 --detect_adapter_for_pe \\
kkonganti@17:                 $args \\
kkonganti@17:                 2> ${prefix}.fastp.log
kkonganti@17: 
kkonganti@17:             cat <<-END_VERSIONS > versions.yml
kkonganti@17:             "${task.process}":
kkonganti@17:                 fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
kkonganti@17:             END_VERSIONS
kkonganti@17:             """
kkonganti@17:     }
kkonganti@17: }