kkonganti@17: process SOURMASH_COMPARE {
kkonganti@17:     tag "Samples vs Genomes"
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:     path queries
kkonganti@17:     path accessions
kkonganti@17: 
kkonganti@17:     output:
kkonganti@17:     path "bcs_sourmash_cont_mat.csv"            , emit: matrix, optional: true
kkonganti@17:     path "bcs_sourmash_cont_mat.data.labels.txt", emit: labels, 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 sm_compare_mode = ("${params.sourmashcompare_mode.split(',')}"
kkonganti@17:         ? "--${params.sourmashcompare_mode.split(',').join(' --')}"
kkonganti@17:         : '')
kkonganti@17:     def sketch_args = (params.sourmashsketch_mode ?: '')
kkonganti@17:     sketch_args += (params.sourmashsketch_singleton ? ' --singleton ' : '')
kkonganti@17:     sketch_args += (params.sourmashsketch_p ? " -p ${params.sourmashsketch_p} " : '')
kkonganti@17:     """
kkonganti@17: 
kkonganti@17:     gen_otf_genome.py \\
kkonganti@17:         -gd "${params.tuspy_gd}" \\
kkonganti@17:         -gds "${params.tuspy_gds}" \\
kkonganti@17:         -txt $accessions
kkonganti@17: 
kkonganti@17:     if [ ! -e "CATTED_GENOMES_FAILED.txt" ]; then
kkonganti@17: 
kkonganti@17:         sourmash sketch \\
kkonganti@17:             $sketch_args \\
kkonganti@17:             --output OTF.db.sig \\
kkonganti@17:             CATTED_GENOMES_scaffolded_genomic.fna.gz
kkonganti@17: 
kkonganti@17:         sourmash compare \\
kkonganti@17:             $sm_compare_mode \\
kkonganti@17:             --${params.sourmashsketch_mode} \\
kkonganti@17:             -k ${params.sourmashgather_k} \\
kkonganti@17:             --csv bcs_sourmash_cont_mat.csv \\
kkonganti@17:             --output bcs_sourmash_cont_mat.data \\
kkonganti@17:             ${queries.collect().join(' ')} \\
kkonganti@17:             OTF.db.sig
kkonganti@17:     fi
kkonganti@17: 
kkonganti@17:     cat <<-END_VERSIONS > versions.yml
kkonganti@17:     "${task.process}":
kkonganti@17:         sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' )
kkonganti@17:         python: \$( python --version | sed 's/Python //g' )
kkonganti@17:         bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
kkonganti@17:     END_VERSIONS
kkonganti@17:     """
kkonganti@17: }