kkonganti@105: process FASTQC {
kkonganti@105:     tag "$meta.id"
kkonganti@105:     label 'process_low'
kkonganti@105: 
kkonganti@105:     module (params.enable_module ? "${params.swmodulepath}${params.fs}fastqc${params.fs}0.11.9" : null)
kkonganti@105:     conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
kkonganti@105:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@105:         'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
kkonganti@105:         'quay.io/biocontainers/fastqc:0.11.9--0' }"
kkonganti@105: 
kkonganti@105:     input:
kkonganti@105:     tuple val(meta), path(reads)
kkonganti@105: 
kkonganti@105:     output:
kkonganti@105:     tuple val(meta), path("*.html"), emit: html
kkonganti@105:     tuple val(meta), path("*.zip") , emit: zip
kkonganti@105:     path  "versions.yml"           , emit: versions
kkonganti@105: 
kkonganti@105:     when:
kkonganti@105:     task.ext.when == null || task.ext.when
kkonganti@105: 
kkonganti@105:     script:
kkonganti@105:     def args = task.ext.args ?: ''
kkonganti@105:     // Add soft-links to original FastQs for consistent naming in pipeline
kkonganti@105:     def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@105:     if (meta.single_end) {
kkonganti@105:         """
kkonganti@105:         [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
kkonganti@105:         fastqc $args --threads $task.cpus ${prefix}.fastq.gz
kkonganti@105: 
kkonganti@105:         cat <<-END_VERSIONS > versions.yml
kkonganti@105:         "${task.process}":
kkonganti@105:             fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
kkonganti@105:         END_VERSIONS
kkonganti@105:         """
kkonganti@105:     } else {
kkonganti@105:         """
kkonganti@105:         [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
kkonganti@105:         [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
kkonganti@105:         fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
kkonganti@105: 
kkonganti@105:         cat <<-END_VERSIONS > versions.yml
kkonganti@105:         "${task.process}":
kkonganti@105:             fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
kkonganti@105:         END_VERSIONS
kkonganti@105:         """
kkonganti@105:     }
kkonganti@105: }