kkonganti@11: process CAT_UNIQUE {
kkonganti@11:     tag "${meta.id}"
kkonganti@11:     label "process_pico"
kkonganti@11: 
kkonganti@11:     module (params.enable_module ? "${params.swmodulepath}${params.fs}perl${params.fs}5.30.0" : null)
kkonganti@11:     conda (params.enable_conda ? "conda-forge::perl conda-forge::coreutils bioconda::perl-bioperl=1.7.8" : null)
kkonganti@11:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@11:         'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1' :
kkonganti@11:         'quay.io/biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }"
kkonganti@11: 
kkonganti@11:     input:
kkonganti@11:         tuple val(meta), path(file)
kkonganti@11: 
kkonganti@11:     output:
kkonganti@11:         path '*_uniq.txt'   , emit: txt
kkonganti@11:         path '*metadata.csv', emit: csv, optional: true
kkonganti@11:         path 'versions.yml' , emit: versions
kkonganti@11: 
kkonganti@11:     when:
kkonganti@11:         task.ext.when == null || task.ext.when
kkonganti@11: 
kkonganti@11:     script:
kkonganti@11:         def args = (task.ext.args ?: '')
kkonganti@11:         def skip = (meta.skip_header ?: 1)
kkonganti@11:         prefix = (task.ext.prefix ?: meta.id)
kkonganti@11:         """
kkonganti@11:         newfile=\$(echo "$file" | sed -e 's/_w_dups/_uniq/g')
kkonganti@11: 
kkonganti@11:         head -n$skip "$file" > \$newfile
kkonganti@11:         tail -n+\$(($skip + 1)) "$file" | sort -n | uniq >> \$newfile
kkonganti@11: 
kkonganti@11:         if [ "\$newfile" == "iTOL_metadata_uniq.txt" ]; then
kkonganti@11:             head -n3 "$file"  | tail -n1 | sed -e 's/^FIELD_LABELS/ID/' > microreact_metadata.csv
kkonganti@11:             tail -n+\$(($skip + 1)) "$file" | sort -n | uniq >> microreact_metadata.csv
kkonganti@11:         fi
kkonganti@11: 
kkonganti@11:         uniqver=""
kkonganti@11: 
kkonganti@11:         if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@11:             uniqver=\$( uniq --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
kkonganti@11:             
kkonganti@11:         else
kkonganti@11:             uniqver=\$( uniq --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
kkonganti@11:         fi
kkonganti@11: 
kkonganti@11:         cat <<-END_VERSIONS > versions.yml
kkonganti@11:         "${task.process}": 
kkonganti@11:             head: \$uniqver
kkonganti@11:             tail: \$uniqver
kkonganti@11:             sort: \$uniqver
kkonganti@11:             uniq: \$uniqver
kkonganti@11:         END_VERSIONS
kkonganti@11:         """
kkonganti@11: }