kkonganti@105: process ABRICATE_SUMMARY {
kkonganti@105:     tag "${abdbs.join(',')}"
kkonganti@105:     label 'process_low'
kkonganti@105: 
kkonganti@105:     module (params.enable_module ? "${params.swmodulepath}${params.fs}abricate${params.fs}1.0.1" : null)
kkonganti@105:     conda (params.enable_conda ? "bioconda::abricate=1.0.1 conda-forge::coreutils" : null)
kkonganti@105:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@105:         'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
kkonganti@105:         'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
kkonganti@105: 
kkonganti@105:     input:
kkonganti@105:     tuple val(abdbs), path(abfiles)
kkonganti@105: 
kkonganti@105:     output:
kkonganti@105:     tuple val('abricate_ncbi'), path("*.ncbi.absum.txt")              , emit: ncbi, optional: true
kkonganti@105:     tuple val('abricate_ncbiamrplus'), path("*.ncbiamrplus.absum.txt"), emit: ncbiamrplus, optional: true
kkonganti@105:     tuple val('abricate_resfinder'), path("*resfinder.absum.txt")     , emit: resfinder, optional: true
kkonganti@105:     tuple val('abricate_megares'), path("*.megares.absum.txt")        , emit: megares, optional: true
kkonganti@105:     tuple val('abricate_argannot'), path("*.argannot.absum.txt")      , emit: argannot, optional: true
kkonganti@105:     tuple val('abricate_ecoli_vf'), path("*.ecoli_vf.absum.txt")      , emit: ecoli_vf, optional: true
kkonganti@105:     path "versions.yml"                                               , emit: versions
kkonganti@105: 
kkonganti@105:     when:
kkonganti@105:     task.ext.when == null || task.ext.when
kkonganti@105: 
kkonganti@105:     script:
kkonganti@105:     def args = task.ext.args ?: ''
kkonganti@105:     def onthese = abdbs.collect{ db ->
kkonganti@105:         abfiles.findAll { files ->
kkonganti@105:             files =~ /\.${db}/
kkonganti@105:         }.join(' ')
kkonganti@105:     }.join('\\n')
kkonganti@105:     """
kkonganti@105:     filenum="1"
kkonganti@105: 
kkonganti@105:     echo -e "$onthese" | while read -r files; do
kkonganti@105:         db=\$( echo -e "\${files}" | grep -E -o '\\w+\\.ab\\.txt' | sort -u | sed -e 's/.ab.txt//' )
kkonganti@105: 
kkonganti@105:         if [ -z "\$db" ]; then
kkonganti@105:             db="\$filenum"
kkonganti@105:         fi
kkonganti@105: 
kkonganti@105:         abricate \\
kkonganti@105:             $args \\
kkonganti@105:             --summary \${files} \\
kkonganti@105:             1> "abricate.\${db}.absum.txt"
kkonganti@105: 
kkonganti@105:         sed -i -e "s/.\${db}.ab.txt//" "abricate.\${db}.absum.txt"
kkonganti@105:         sed -i -e 's/.assembly_filtered_contigs.fasta//' "abricate.\${db}.absum.txt"
kkonganti@105: 
kkonganti@105:         filenum=\$((filenum+1))
kkonganti@105:     done
kkonganti@105: 
kkonganti@105:     cat <<-END_VERSIONS > versions.yml
kkonganti@105:     "${task.process}":
kkonganti@105:         abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
kkonganti@105:         bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
kkonganti@105:     END_VERSIONS
kkonganti@105: 
kkonganti@105:     sedver=""
kkonganti@105:     sortver=""
kkonganti@105:     grepver=""
kkonganti@105: 
kkonganti@105:     if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@105:         sortver=\$( sort --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
kkonganti@105:         sedver="\$sortver"
kkonganti@105:         grepver="\$sortver"
kkonganti@105:     else
kkonganti@105:         sortver=\$( sort --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:         grepver=\$( echo \$(grep --version 2>&1) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
kkonganti@105:     fi
kkonganti@105: 
kkonganti@105:     cat <<-END_VERSIONS >> versions.yml
kkonganti@105:         sort: \$sortver
kkonganti@105:         grep: \$grepver
kkonganti@105:         sed: \$sedver
kkonganti@105:     END_VERSIONS
kkonganti@105:     """
kkonganti@105: }