kkonganti@17: process KMA_INDEX {
kkonganti@17:     tag "$meta.id"
kkonganti@17:     label 'process_nano'
kkonganti@17: 
kkonganti@17:     module (params.enable_module ? "${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 conda-forge::coreutils" : null)
kkonganti@17:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@17:         'https://depot.galaxyproject.org/singularity/kma:1.4.3--h7132678_1':
kkonganti@17:         'quay.io/biocontainers/kma:1.4.3--h7132678_1' }"
kkonganti@17: 
kkonganti@17:     input:
kkonganti@17:         tuple val(meta), path(fasta)
kkonganti@17: 
kkonganti@17:     output:
kkonganti@17:         tuple val(meta), path("${meta.id}_kma_idx"), emit: idx
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}_kma_idx"
kkonganti@17:         def add_to_db = (meta.kmaindex_t_db ? "-t_db ${meta.kmaindex_t_db}" : '')
kkonganti@17:         """
kkonganti@17:         mkdir -p $prefix && cd $prefix || exit 1
kkonganti@17:         kma \\
kkonganti@17:             index \\
kkonganti@17:             $args \\
kkonganti@17:             $add_to_db \\
kkonganti@17:             -i ../$fasta \\
kkonganti@17:             -o $prefix
kkonganti@17:         cd .. || exit 1
kkonganti@17: 
kkonganti@17:         cat <<-END_VERSIONS > versions.yml
kkonganti@17:         "${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: 
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:         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:         fi
kkonganti@17: 
kkonganti@17:         cat <<-END_VERSIONS >> versions.yml
kkonganti@17:             mkdir: \$mkdirver
kkonganti@17:             cut: \$cutver
kkonganti@17:             cd: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
kkonganti@17:         END_VERSIONS
kkonganti@17:         """
kkonganti@17: }