kkonganti@17: process KMA_ALIGN {
kkonganti@17:     tag "$meta.id"
kkonganti@17:     label 'process_micro'
kkonganti@17: 
kkonganti@17:     module (params.enable_module ? "${params.swmodulepath}${params.fs}kma${params.fs}1.4.4" : null)
kkonganti@17:     conda (params.enable_conda ? "conda-forge::libgcc-ng bioconda::kma=1.4.3" : null)
kkonganti@17:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@17:         'https://depot.galaxyproject.org/singularity/kma:1.4.3--h7132678_1':
kkonganti@17:         'quay.io/biocontainers/kma:1.4.3--h7132678_1' }"
kkonganti@17: 
kkonganti@17:     input:
kkonganti@17:         tuple val(meta), path(reads), path(index)
kkonganti@17: 
kkonganti@17:     output:
kkonganti@17:         path "${meta.id}_kma_res"
kkonganti@17:         tuple val(meta), path("${meta.id}_kma_res${params.fs}*.res")              , emit: res
kkonganti@17:         tuple val(meta), path("${meta.id}_kma_res${params.fs}*.mapstat")          , emit: mapstat, optional: true
kkonganti@17:         tuple val(meta), path("${meta.id}_kma_res${params.fs}*.frag.gz")          , emit: frags, optional: true
kkonganti@17:         tuple val(meta), path("${meta.id}_kma_res${params.fs}*_template_hits.txt"), emit: hits, optional: true
kkonganti@17:         path "versions.yml"                                                       , emit: versions
kkonganti@17: 
kkonganti@17:     when:
kkonganti@17:         task.ext.when == null || task.ext.when
kkonganti@17: 
kkonganti@17:     script:
kkonganti@17:         def args = task.ext.args ?: ''
kkonganti@17:         def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@17:         def reads_in = (meta.single_end ? "-i $reads" : "-ipe ${reads[0]} ${reads[1]}")
kkonganti@17:         def db = (meta.kma_t_db ?: "${index}")
kkonganti@17:         def db_basename = (db ? "${index.baseName}" : '')
kkonganti@17:         def get_hit_accs = (meta.get_kma_hit_accs ? 'true' : 'false')
kkonganti@17:         def res_dir = prefix + '_kma_res'
kkonganti@17:         reads_in = (params.kmaalign_int ? "-int $reads" : "-i $reads")
kkonganti@17:         """
kkonganti@17:         mkdir -p $res_dir || exit 1
kkonganti@17:         kma \\
kkonganti@17:             $args \\
kkonganti@17:             -t_db $db${params.fs}$db_basename \\
kkonganti@17:             -t $task.cpus \\
kkonganti@17:             -o $res_dir${params.fs}$prefix \\
kkonganti@17:             $reads_in
kkonganti@17: 
kkonganti@17:         if [ "$get_hit_accs" == "true" ]; then
kkonganti@17:             grep -v '^#' $res_dir${params.fs}${prefix}.res | \\
kkonganti@17:                 grep -E -o 'GC[AF]\\_[0-9]+\\.*[0-9]*' > $res_dir${params.fs}${prefix}_template_hits.txt
kkonganti@17:         fi
kkonganti@17: 
kkonganti@17:         cat <<-END_VERSIONS > versions.yml
kkonganti@17:         "${task.process}":
kkonganti@17:             kma: \$( kma -v | sed -e 's%KMA-%%' )
kkonganti@17:         END_VERSIONS
kkonganti@17: 
kkonganti@17:         mkdirver=""
kkonganti@17:         cutver=""
kkonganti@17:         grepver=""
kkonganti@17: 
kkonganti@17:         if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@17:             mkdirver=\$( mkdir --help 2>&1 | sed -e '1!d; s/ (.*\$//' |  cut -f1-2 -d' ' )
kkonganti@17:             cutver="\$mkdirver"
kkonganti@17:             grepver="\$mkdirver"
kkonganti@17:         else
kkonganti@17:             mkdirver=\$( mkdir --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
kkonganti@17:             cutver=\$( cut --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
kkonganti@17:             grepver=\$( echo \$(grep --version 2>&1) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
kkonganti@17:         fi
kkonganti@17: 
kkonganti@17:         cat <<-END_VERSIONS >> versions.yml
kkonganti@17:             mkdir: \$mkdirver
kkonganti@17:             cut: \$cutver
kkonganti@17:             grep: \$grepver
kkonganti@17:         END_VERSIONS
kkonganti@17:         """
kkonganti@17: }