kkonganti@1: process SALMON_INDEX {
kkonganti@1:     tag "$meta.id"
kkonganti@1:     label "process_low"
kkonganti@1: 
kkonganti@1:     module (params.enable_module ? "${params.swmodulepath}${params.fs}salmon${params.fs}1.9.0" : null)
kkonganti@9:     conda (params.enable_conda ? 'conda-forge::libgcc-ng bioconda::salmon=1.10.1' : null)
kkonganti@1:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@1:         'https://depot.galaxyproject.org/singularity/salmon:1.9.0--h7e5ed60_1' :
kkonganti@1:         'quay.io/biocontainers/salmon:1.9.0--h7e5ed60_1' }"
kkonganti@1: 
kkonganti@1:     input:
kkonganti@1:         tuple val(meta), path(genome_fasta)
kkonganti@1: 
kkonganti@1:     output:
kkonganti@1:         tuple val(meta), path("${meta.id}_salmon_idx"), emit: idx
kkonganti@1:         path "versions.yml"                           , emit: versions
kkonganti@1: 
kkonganti@1:     when:
kkonganti@1:         task.ext.when == null || task.ext.when
kkonganti@1: 
kkonganti@1:     script:
kkonganti@1:         def args = task.ext.args ?: ''
kkonganti@1:         def prefix = task.ext.prefix ?: "${meta.id}_salmon_idx"
kkonganti@1:         def decoys_file = file( meta.salmon_decoys )
kkonganti@1:         def decoys = !("${decoys_file.simpleName}" ==~ 'dummy_file.*') && decoys_file.exits() ? "--decoys ${meta.salmon_decoys}" : ''
kkonganti@1:         """
kkonganti@1:         salmon \\
kkonganti@1:             index \\
kkonganti@1:             $decoys \\
kkonganti@1:             --threads $task.cpus \\
kkonganti@1:             $args \\
kkonganti@1:             --index $prefix \\
kkonganti@1:             --transcripts $genome_fasta
kkonganti@1: 
kkonganti@1:         cat <<-END_VERSIONS > versions.yml
kkonganti@1:         "${task.process}":
kkonganti@1:             salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
kkonganti@1:         END_VERSIONS
kkonganti@1:         """
kkonganti@1: }