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1 process SALMON_QUANT {
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2 tag "$meta.id"
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3 label "process_medium"
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}salmon${params.fs}1.9.0" : null)
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6 conda (params.enable_conda ? 'conda-forge::libgcc-ng bioconda::salmon=1.9.0' : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/salmon:1.9.0--h7e5ed60_1' :
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9 'quay.io/biocontainers/salmon:1.9.0--h7e5ed60_1' }"
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10 input:
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11 tuple val(meta), path(reads_or_bam), path(index_or_tr_fasta)
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12
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13 output:
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14 tuple val(meta), path("${meta.id}_salmon_res"), emit: results
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15 path "versions.yml" , emit: versions
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16
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17 when:
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18 task.ext.when == null || task.ext.when
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19
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20 script:
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21 def args = task.ext.args ?: ''
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22 def prefix = task.ext.prefix ?: "${meta.id}_salmon_res"
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23 def reference = "--index $index_or_tr_fasta"
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24 def lib_type = (meta.salmon_lib_type ?: '')
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25 def alignment_mode = (meta.salmon_alignment_mode ?: '')
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26 def gtf = (meta.salmon_gtf ? "--geneMap ${meta.salmon_gtf}" : '')
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27 def input_reads =(meta.single_end ? "-r $reads_or_bam" : "-1 ${reads_or_bam[0]} -2 ${reads_or_bam[1]}")
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28
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29 // Use path(reads_or_bam) to point to BAM and path(index_or_tr_fasta) to point to transcript fasta
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30 // if using salmon DSL2 module in alignment-based mode.
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31 // By default, this module will be run in selective-alignment-based mode of salmon.
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32 if (alignment_mode) {
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33 reference = "-t $index_or_tr_fasta"
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34 input_reads = "-a $reads_or_bam"
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35 }
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36
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37 def strandedness_opts = [
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38 'A', 'U', 'SF', 'SR',
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39 'IS', 'IU' , 'ISF', 'ISR',
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40 'OS', 'OU' , 'OSF', 'OSR',
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41 'MS', 'MU' , 'MSF', 'MSR'
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42 ]
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43
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44 def strandedness = 'A'
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45
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46 if (lib_type) {
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47 if (strandedness_opts.contains(lib_type)) {
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48 strandedness = lib_type
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49 } else {
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50 log.info "[Salmon Quant] Invalid library type specified '--libType=${lib_type}', defaulting to auto-detection with '--libType=A'."
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51 }
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52 } else {
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53 strandedness = meta.single_end ? 'U' : 'IU'
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54 if (meta.strandedness == 'forward') {
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55 strandedness = meta.single_end ? 'SF' : 'ISF'
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56 } else if (meta.strandedness == 'reverse') {
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57 strandedness = meta.single_end ? 'SR' : 'ISR'
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58 }
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59 }
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60 """
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61 salmon quant \\
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62 --threads $task.cpus \\
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63 --libType=$strandedness \\
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64 $gtf \\
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65 $args \\
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66 -o $prefix \\
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67 $reference \\
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68 $input_reads
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69
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70 cat <<-END_VERSIONS > versions.yml
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71 "${task.process}":
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72 salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
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73 END_VERSIONS
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74 """
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75 } |
