kkonganti@17: process SOURMASH_GATHER {
kkonganti@17:     tag "$meta.id"
kkonganti@17:     label 'process_micro'
kkonganti@17: 
kkonganti@17:     module (params.enable_module ? "${params.swmodulepath}${params.fs}sourmash${params.fs}4.6.1" : null)
kkonganti@17:     conda (params.enable_conda ? "conda-forge::python bioconda::sourmash=4.6.1" : null)
kkonganti@17:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@17:         'https://depot.galaxyproject.org/singularity/sourmash:4.6.1--hdfd78af_0':
kkonganti@17:         'quay.io/biocontainers/sourmash:4.6.1--hdfd78af_0' }"
kkonganti@17: 
kkonganti@17:     input:
kkonganti@17:     tuple val(meta), path(signature), path(database)
kkonganti@17:     val save_unassigned
kkonganti@17:     val save_matches_sig
kkonganti@17:     val save_prefetch
kkonganti@17:     val save_prefetch_csv
kkonganti@17: 
kkonganti@17:     output:
kkonganti@17:     tuple val(meta), path("*.csv.gz")                   , emit: result       , optional: true
kkonganti@17:     tuple val(meta), path("*_scaffolded_genomic.fna.gz"), emit: genomes_fasta, optional: true
kkonganti@17:     tuple val(meta), path("*_unassigned.sig.zip")       , emit: unassigned   , optional: true
kkonganti@17:     tuple val(meta), path("*_matches.sig.zip")          , emit: matches      , optional: true
kkonganti@17:     tuple val(meta), path("*_prefetch.sig.zip")         , emit: prefetch     , optional: true
kkonganti@17:     tuple val(meta), path("*_prefetch.csv.gz")          , emit: prefetchcsv  , optional: true
kkonganti@17:     path "*FAILED.txt"                                  , emit: failed       , optional: true
kkonganti@17:     path "versions.yml"                                 , emit: versions
kkonganti@17: 
kkonganti@17:     when:
kkonganti@17:     task.ext.when == null || task.ext.when
kkonganti@17: 
kkonganti@17:     script:
kkonganti@17:     def args        = task.ext.args ?: ''
kkonganti@17:     def args2       = task.ext.args2 ?: ''
kkonganti@17:     def prefix      = task.ext.prefix ?: "${meta.id}"
kkonganti@17:     def unassigned  = save_unassigned   ? "--output-unassigned ${prefix}_unassigned.sig.zip" : ''
kkonganti@17:     def matches     = save_matches_sig  ? "--save-matches ${prefix}_matches.sig.zip"         : ''
kkonganti@17:     def prefetch    = save_prefetch     ? "--save-prefetch ${prefix}_prefetch.sig.zip"       : ''
kkonganti@17:     def prefetchcsv = save_prefetch_csv ? "--save-prefetch-csv ${prefix}_prefetch.csv.gz"    : ''
kkonganti@17:     def gd          = params.tuspy_gd   ? "-gd ${params.tuspy_gd}"                           : ''
kkonganti@17: 
kkonganti@17:     """
kkonganti@17:     sourmash gather \\
kkonganti@17:         $args \\
kkonganti@17:         --output ${prefix}.csv.gz \\
kkonganti@17:         ${unassigned} \\
kkonganti@17:         ${matches} \\
kkonganti@17:         ${prefetch} \\
kkonganti@17:         ${prefetchcsv} \\
kkonganti@17:         ${signature} \\
kkonganti@17:         ${database}
kkonganti@17: 
kkonganti@17:     sourmash_filter_hits.py \\
kkonganti@17:         $args2 \\
kkonganti@17:         -csv ${prefix}.csv.gz
kkonganti@17: 
kkonganti@17:     gen_otf_genome.py \\
kkonganti@17:         $gd \\
kkonganti@17:         -op ${prefix} \\
kkonganti@17:         -txt ${prefix}_template_hits.txt
kkonganti@17: 
kkonganti@17:     cat <<-END_VERSIONS > versions.yml
kkonganti@17:     "${task.process}":
kkonganti@17:         sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' )
kkonganti@17:         python: \$( python --version | sed 's/Python //g' )
kkonganti@17:     END_VERSIONS
kkonganti@17:     """
kkonganti@17: }