kkonganti@17: process DB_PER_SNP_CLUSTER {
kkonganti@17:     tag "waterfall_per_snp_cluster.pl"
kkonganti@17:     label "process_pico"
kkonganti@17: 
kkonganti@17:     module (params.enable_module ? "${params.swmodulepath}${params.fs}perl${params.fs}5.30.0" : null)
kkonganti@17:     conda (params.enable_conda ? "conda-forge::perl bioconda::perl-bioperl=1.7.8" : null)
kkonganti@17:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@17:         'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1' :
kkonganti@17:         'quay.io/biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }"
kkonganti@17: 
kkonganti@17:     input:
kkonganti@17:         path accs_tbl
kkonganti@17:         path pdg_metadata
kkonganti@17:         path snp_cluster_metadata
kkonganti@17: 
kkonganti@17:     output:
kkonganti@17:         path '*asm_chunk_snp.tbl'       , emit: asm_chunk_snp_tbl
kkonganti@17:         path '*asm_chunk_snp_counts.tbl', emit: asm_chunk_snp_counts
kkonganti@17:         path '*accs_snp.txt'            , emit: accs_snp
kkonganti@17:         path 'mash_snp_genome_list.txt' , emit: genome_paths
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.index ?: ''
kkonganti@17:         """
kkonganti@17:         waterfall_per_snp_cluster.pl \\
kkonganti@17:             -p $pdg_metadata \\
kkonganti@17:             -tb $accs_tbl \\
kkonganti@17:             -snp $snp_cluster_metadata \\
kkonganti@17:             $args \\
kkonganti@17:             1> asm_chunk_snp.tbl 2> asm_chunk_snp_counts.tbl
kkonganti@17: 
kkonganti@17:         cat <<-END_VERSIONS > versions.yml
kkonganti@17:         "${task.process}":
kkonganti@17:             perl: \$( perl -e 'print \$^V' | sed 's/v//g' )
kkonganti@17:             bioperl: \$(perl -MBio::Root::Version -e 'print \$Bio::Root::Version::VERSION')
kkonganti@17:         END_VERSIONS
kkonganti@17:         """
kkonganti@17: }