kkonganti@0: process QUAST {
kkonganti@0:     tag "$meta.id"
kkonganti@0:     label "process_micro"
kkonganti@0: 
kkonganti@0:     module (params.enable_module ? "${params.swmodulepath}${params.fs}quast${params.fs}5.2.0" : null)
kkonganti@0:     conda (params.enable_conda ? "bioconda::quast=5.2.0 conda-forge::libgcc-ng" : null)
kkonganti@0:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@0:         'https://depot.galaxyproject.org/singularity/quast:5.2.0--py39pl5321h2add14b_1' :
kkonganti@0:         'biocontainers/quast:5.2.0--py39pl5321h2add14b_1' }"
kkonganti@0: 
kkonganti@0:     input:
kkonganti@0:         tuple val(meta) , path(consensus)
kkonganti@0:         tuple val(meta2), path(fasta)
kkonganti@0:         tuple val(meta3), path(gff)
kkonganti@0: 
kkonganti@0:     output:
kkonganti@0:         tuple val(meta), path("${prefix}")                  , emit: results
kkonganti@0:         tuple val(meta), path("${prefix}.quastreport.tsv")  , emit: tsv
kkonganti@0:         tuple val(meta), path("${prefix}_transcriptome.tsv"), emit: transcriptome, optional: true
kkonganti@0:         tuple val(meta), path("${prefix}_misassemblies.tsv"), emit: misassemblies, optional: true
kkonganti@0:         tuple val(meta), path("${prefix}_unaligned.tsv")    , emit: unaligned    , optional: true
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:         prefix        = task.ext.prefix ?: "${meta.id}"
kkonganti@0:         def reference = fasta ? "-r $fasta" : ''
kkonganti@0:         def features  = gff ?  "--features $gff" : ''
kkonganti@0:         """
kkonganti@0:         quast.py \\
kkonganti@0:             -l $prefix \\
kkonganti@0:             --output-dir $prefix \\
kkonganti@0:             $reference \\
kkonganti@0:             $features \\
kkonganti@0:             --threads $task.cpus \\
kkonganti@0:             $args \\
kkonganti@0:             ${consensus.join(' ')}
kkonganti@0: 
kkonganti@0:         ln -s ${prefix}/report.tsv ${prefix}.quastreport.tsv
kkonganti@0:         [ -f  ${prefix}/contigs_reports/all_alignments_transcriptome.tsv ] && ln -s ${prefix}/contigs_reports/all_alignments_transcriptome.tsv ${prefix}_transcriptome.tsv
kkonganti@0:         [ -f  ${prefix}/contigs_reports/misassemblies_report.tsv         ] && ln -s ${prefix}/contigs_reports/misassemblies_report.tsv ${prefix}_misassemblies.tsv
kkonganti@0:         [ -f  ${prefix}/contigs_reports/unaligned_report.tsv             ] && ln -s ${prefix}/contigs_reports/unaligned_report.tsv ${prefix}_unaligned.tsv
kkonganti@0: 
kkonganti@0:         cat <<-END_VERSIONS > versions.yml
kkonganti@0:         "${task.process}":
kkonganti@0:             quast: \$(quast.py --version 2>&1 | sed 's/^.*QUAST v//; s/ .*\$//')
kkonganti@0:             bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
kkonganti@0:         END_VERSIONS
kkonganti@0: 
kkonganti@0:         zcmd=""
kkonganti@0:         zver=""
kkonganti@0: 
kkonganti@0:         if type pigz > /dev/null 2>&1; then
kkonganti@0:             zcmd="pigz"
kkonganti@0:             zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
kkonganti@0:         elif type gzip > /dev/null 2>&1; then
kkonganti@0:             zcmd="gzip"
kkonganti@0:         
kkonganti@0:             if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@0:                 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
kkonganti@0:             else
kkonganti@0:                 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
kkonganti@0:             fi
kkonganti@0:         fi
kkonganti@0: 
kkonganti@0:         cat <<-END_VERSIONS >> versions.yml
kkonganti@0:             \$zcmd: \$zver
kkonganti@0:         END_VERSIONS
kkonganti@0:         """
kkonganti@0: }