kkonganti@1: process SALMON_QUANT {
kkonganti@1:     tag "$meta.id"
kkonganti@1:     label "process_medium"
kkonganti@1: 
kkonganti@1:     module (params.enable_module ? "${params.swmodulepath}${params.fs}salmon${params.fs}1.9.0" : null)
kkonganti@1:     conda (params.enable_conda ? 'conda-forge::libgcc-ng bioconda::salmon=1.9.0' : null)
kkonganti@1:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@1:         'https://depot.galaxyproject.org/singularity/salmon:1.9.0--h7e5ed60_1' :
kkonganti@1:         'quay.io/biocontainers/salmon:1.9.0--h7e5ed60_1' }"
kkonganti@1:     input:
kkonganti@1:         tuple val(meta), path(reads_or_bam), path(index_or_tr_fasta)
kkonganti@1: 
kkonganti@1:     output:
kkonganti@1:         tuple val(meta), path("${meta.id}_salmon_res"), emit: results
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_res"
kkonganti@1:         def reference   = "--index $index_or_tr_fasta"
kkonganti@1:         def lib_type = (meta.salmon_lib_type ?: '')
kkonganti@1:         def alignment_mode = (meta.salmon_alignment_mode ?: '')
kkonganti@1:         def gtf = (meta.salmon_gtf ? "--geneMap ${meta.salmon_gtf}" : '')
kkonganti@1:         def input_reads =(meta.single_end ? "-r $reads_or_bam" : "-1 ${reads_or_bam[0]} -2 ${reads_or_bam[1]}")
kkonganti@1: 
kkonganti@1:         // Use path(reads_or_bam) to point to BAM and path(index_or_tr_fasta) to point to transcript fasta
kkonganti@1:         // if using salmon DSL2 module in alignment-based mode.
kkonganti@1:         // By default, this module will be run in selective-alignment-based mode of salmon.
kkonganti@1:         if (alignment_mode) {
kkonganti@1:             reference   = "-t $index_or_tr_fasta"
kkonganti@1:             input_reads = "-a $reads_or_bam"
kkonganti@1:         }
kkonganti@1: 
kkonganti@1:         def strandedness_opts = [
kkonganti@1:             'A', 'U', 'SF', 'SR',
kkonganti@1:             'IS', 'IU' , 'ISF', 'ISR',
kkonganti@1:             'OS', 'OU' , 'OSF', 'OSR',
kkonganti@1:             'MS', 'MU' , 'MSF', 'MSR'
kkonganti@1:         ]
kkonganti@1: 
kkonganti@1:         def strandedness =  'A'
kkonganti@1: 
kkonganti@1:         if (lib_type) {
kkonganti@1:             if (strandedness_opts.contains(lib_type)) {
kkonganti@1:                 strandedness = lib_type
kkonganti@1:             } else {
kkonganti@1:                 log.info "[Salmon Quant] Invalid library type specified '--libType=${lib_type}', defaulting to auto-detection with '--libType=A'."
kkonganti@1:             }
kkonganti@1:         } else {
kkonganti@1:             strandedness = meta.single_end ? 'U' : 'IU'
kkonganti@1:             if (meta.strandedness == 'forward') {
kkonganti@1:                 strandedness = meta.single_end ? 'SF' : 'ISF'
kkonganti@1:             } else if (meta.strandedness == 'reverse') {
kkonganti@1:                 strandedness = meta.single_end ? 'SR' : 'ISR'
kkonganti@1:             }
kkonganti@1:         }
kkonganti@1:         """
kkonganti@1:         salmon quant \\
kkonganti@1:             --threads $task.cpus \\
kkonganti@1:             --libType=$strandedness \\
kkonganti@1:             $gtf \\
kkonganti@1:             $args \\
kkonganti@1:             -o $prefix \\
kkonganti@1:             $reference \\
kkonganti@1:             $input_reads
kkonganti@1: 
kkonganti@1:         cat <<-END_VERSIONS > versions.yml
kkonganti@1:         "${task.process}":
kkonganti@1:             salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
kkonganti@1:         END_VERSIONS
kkonganti@1:         """
kkonganti@1: }