kkonganti@17: process SOURMASH_SKETCH {
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@17:         'https://depot.galaxyproject.org/singularity/sourmash:4.6.1--hdfd78af_0':
kkonganti@17:         'quay.io/biocontainers/sourmash:4.6.1--hdfd78af_0' }"
kkonganti@17: 
kkonganti@17:     input:
kkonganti@17:     tuple val(meta), path(sequence), path(database)
kkonganti@17: 
kkonganti@17:     output:
kkonganti@17:     tuple val(meta), path("*.query.sig"), path("*.db.sig"), emit: signatures
kkonganti@17:     path "versions.yml"                                   , emit: versions
kkonganti@17: 
kkonganti@17:     when:
kkonganti@17:     task.ext.when == null || task.ext.when
kkonganti@17: 
kkonganti@17:     script:
kkonganti@17:     // required defaults for the tool to run, but can be overridden
kkonganti@17:     def args = task.ext.args ?: ''
kkonganti@17:     def args_query 
kkonganti@17:     def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@17:     """
kkonganti@17:     sourmash sketch \\
kkonganti@17:         ${args.toString().replace('--singleton', '')} \\
kkonganti@17:         --output "${prefix}.query.pre" \\
kkonganti@17:         $sequence
kkonganti@17: 
kkonganti@17:     sourmash signature rename \\
kkonganti@17:         --${args.toString().replaceAll(/\s+\-p.*/, '')} \\
kkonganti@17:         -o "${prefix}.query.sig" \\
kkonganti@17:         "${prefix}.query.pre" \\
kkonganti@17:         ${prefix} 
kkonganti@17: 
kkonganti@17:     sourmash sketch \\
kkonganti@17:         $args \\
kkonganti@17:         --output "${prefix}.db.sig" \\
kkonganti@17:         $database
kkonganti@17: 
kkonganti@17:     cat <<-END_VERSIONS > versions.yml
kkonganti@17:     "${task.process}":
kkonganti@17:         sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' )
kkonganti@17:     END_VERSIONS
kkonganti@17:     """
kkonganti@17: }