kkonganti@105: process CENTRIFUGE_EXTRACT {
kkonganti@105:     tag "$meta.id"
kkonganti@105:     label 'process_low'
kkonganti@105: 
kkonganti@105:     //seqkit container contains required bash and other utilities
kkonganti@105:     module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
kkonganti@105:     conda (params.enable_conda ? "conda-forge::sed=4.7 conda-forge::coreutils" : null)
kkonganti@105:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@105:         'https://depot.galaxyproject.org/singularity/mulled-v2-039542721b6b463b663872ba8b7e9fbc05f01925:1de88053ebf8fb9884758395c4871f642c57750c-0':
kkonganti@105:         'quay.io/biocontainers/mulled-v2-039542721b6b463b663872ba8b7e9fbc05f01925:1de88053ebf8fb9884758395c4871f642c57750c-0' }"
kkonganti@105: 
kkonganti@105:     input:
kkonganti@105:     tuple val(meta), path(centrifuge_report)
kkonganti@105:     tuple val(meta), path(centrifuge_output)
kkonganti@105: 
kkonganti@105:     output:
kkonganti@105:     tuple val(meta), path('*.extract-centrifuge-bug-ids.txt'), emit: extracted
kkonganti@105:     path "versions.yml"                                      , emit: versions
kkonganti@105: 
kkonganti@105:     when:
kkonganti@105:     task.ext.when == null || task.ext.when
kkonganti@105: 
kkonganti@105:     script:
kkonganti@105:     def args = task.ext.args ?: ''
kkonganti@105:     def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@105:     """
kkonganti@105:     grep -F '${params.centrifuge_extract_bug}' $centrifuge_report \
kkonganti@105:         | cut -f2 \
kkonganti@105:         | sort -u \
kkonganti@105:         | while read -r taxId; do
kkonganti@105:             echo -e "\t\$taxId"'\$'
kkonganti@105:         done > gotcha.txt
kkonganti@105: 
kkonganti@105:     cut -f1-3 $centrifuge_output | grep -E -f gotcha.txt | cut -f1 | sort -u > ${prefix}.extract-centrifuge-bug-ids.txt || true
kkonganti@105: 
kkonganti@105:     cat <<-END_VERSIONS > versions.yml
kkonganti@105:     "${task.process}":
kkonganti@105:         bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
kkonganti@105:     END_VERSIONS
kkonganti@105: 
kkonganti@105:     ver=""
kkonganti@105:     sedver=""
kkonganti@105: 
kkonganti@105:     if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@105:         ver=\$( cut --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
kkonganti@105:         sedver="\$ver"
kkonganti@105:     else
kkonganti@105:         ver=\$( cut --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
kkonganti@105:         sedver=\$( echo \$(sed --version 2>&1) | sed 's/^.*(GNU sed) //; s/ Copyright.*\$//' )
kkonganti@105:     fi
kkonganti@105: 
kkonganti@105:     cat <<-END_VERSIONS >> versions.yml
kkonganti@105:         cut: \$ver
kkonganti@105:         tail: \$ver
kkonganti@105:         sort: \$ver
kkonganti@105:         sed: \$sedver
kkonganti@105:     END_VERSIONS
kkonganti@105:     """
kkonganti@105: }