kkonganti@17: process SOURMASH_SIG_KMERS {
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@17:         'https://depot.galaxyproject.org/singularity/sourmash:4.6.1--hdfd78af_0' :
kkonganti@17:         'quay.io/biocontainers/sourmash:4.6.1--hdfd78af_0' }"
kkonganti@17: 
kkonganti@17:     input:
kkonganti@17:         tuple val(meta), path(sig_or_seq), path(sequence)
kkonganti@17: 
kkonganti@17:     output:
kkonganti@17:         tuple val(meta), path("*.csv")  , emit: signatures, optional: true
kkonganti@17:         tuple val(meta), path("*.fasta"), emit: extracted_fasta, optional: true
kkonganti@17:         path "versions.yml"             , emit: versions
kkonganti@17: 
kkonganti@17:     when:
kkonganti@17:         task.ext.when == null || task.ext.when
kkonganti@17: 
kkonganti@17:     script:
kkonganti@17:         // required defaults for the tool to run, but can be overridden
kkonganti@17:         def args = task.ext.args ?: ''
kkonganti@17:         def is_seq = "${sig_or_seq.baseName.findAll(/(?i)\.(fa|fasta|fna)\.{0,1}(gz){0,1}$/).size()}"
kkonganti@17:         def save_kmers = (params.sourmashsigkmers_save_kmers ? "--save-kmers ${meta.id}.sm.kmers.csv" : '')
kkonganti@17:         def save_seqs = (params.sourmashsigkmers_save_seqs ? "--save-sequences ${meta.id}.sm.seq.fasta" : '')
kkonganti@17:         def sketch_mode = (params.sourmashsketch_mode ?: 'dna')
kkonganti@17:         def sketch_p = (params.sourmashsketch_p ?: "abund,scaled=1000,k=71")
kkonganti@17:         def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@17:         """
kkonganti@17:         db_sig="${sig_or_seq}"
kkonganti@17:         if [[ $is_seq -ge 1 ]]; then
kkonganti@17:             db_sig="${prefix}.db.sig"
kkonganti@17:             sourmash sketch \\
kkonganti@17:                 $sketch_mode \\
kkonganti@17:                 -p '$sketch_p' \\
kkonganti@17:                 --output \$db_sig \\
kkonganti@17:                 $sig_or_seq
kkonganti@17:         fi
kkonganti@17: 
kkonganti@17:         sourmash signature kmers \\
kkonganti@17:             $args \\
kkonganti@17:             $save_kmers \\
kkonganti@17:             $save_seqs \\
kkonganti@17:             --signatures \$db_sig \\
kkonganti@17:             --sequences $sequence 
kkonganti@17: 
kkonganti@17:         cat <<-END_VERSIONS > versions.yml
kkonganti@17:         "${task.process}":
kkonganti@17:             sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' )
kkonganti@17:             bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
kkonganti@17:         END_VERSIONS
kkonganti@17:         """
kkonganti@17: }