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1 process QUAST {
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2 tag "$meta.id"
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3 label "process_micro"
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}quast${params.fs}5.2.0" : null)
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6 conda (params.enable_conda ? "bioconda::quast=5.2.0 conda-forge::libgcc-ng" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/quast:5.2.0--py39pl5321h2add14b_1' :
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9 'quay.io/biocontainers/quast:5.2.0--py39pl5321h2add14b_1' }"
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10
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11 input:
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12 tuple val(meta) , path(consensus)
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13 tuple val(meta2), path(fasta)
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14 tuple val(meta3), path(gff)
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15
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16 output:
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17 tuple val(meta), path("${prefix}") , emit: results
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18 tuple val(meta), path("${prefix}.quastreport.tsv") , emit: tsv
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19 tuple val(meta), path("${prefix}_transcriptome.tsv"), emit: transcriptome, optional: true
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20 tuple val(meta), path("${prefix}_misassemblies.tsv"), emit: misassemblies, optional: true
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21 tuple val(meta), path("${prefix}_unaligned.tsv") , emit: unaligned , optional: true
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22 path "versions.yml" , emit: versions
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23
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24 when:
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25 task.ext.when == null || task.ext.when
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26
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27 script:
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28 def args = task.ext.args ?: ''
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29 prefix = task.ext.prefix ?: "${meta.id}"
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30 def reference = fasta ? "-r $fasta" : ''
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31 def features = gff ? "--features $gff" : ''
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32 """
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33 quast.py \\
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34 -l $prefix \\
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35 --output-dir $prefix \\
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36 $reference \\
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37 $features \\
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38 --threads $task.cpus \\
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39 $args \\
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40 ${consensus.join(' ')}
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41
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42 ln -s ${prefix}/report.tsv ${prefix}.quastreport.tsv
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43 [ -f ${prefix}/contigs_reports/all_alignments_transcriptome.tsv ] && ln -s ${prefix}/contigs_reports/all_alignments_transcriptome.tsv ${prefix}_transcriptome.tsv
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44 [ -f ${prefix}/contigs_reports/misassemblies_report.tsv ] && ln -s ${prefix}/contigs_reports/misassemblies_report.tsv ${prefix}_misassemblies.tsv
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45 [ -f ${prefix}/contigs_reports/unaligned_report.tsv ] && ln -s ${prefix}/contigs_reports/unaligned_report.tsv ${prefix}_unaligned.tsv
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46
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47 cat <<-END_VERSIONS > versions.yml
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48 "${task.process}":
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49 quast: \$(quast.py --version 2>&1 | sed 's/^.*QUAST v//; s/ .*\$//')
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50 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
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51 END_VERSIONS
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52
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53 zcmd=""
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54 zver=""
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55
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56 if type pigz > /dev/null 2>&1; then
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57 zcmd="pigz"
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58 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
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59 elif type gzip > /dev/null 2>&1; then
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60 zcmd="gzip"
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61
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62 if [ "${workflow.containerEngine}" != "null" ]; then
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63 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d; s/^.*\$zcmd //; s/ Copyright.*\$//' )
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64 else
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65 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
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66 fi
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67 fi
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68
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69 cat <<-END_VERSIONS >> versions.yml
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70 \$zcmd: \$zver
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71 END_VERSIONS
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72 """
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73 } |
