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1 process NOWAYOUT_RESULTS {
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2 tag "nowayout aggregate"
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3 label "process_pico"
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
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6 conda (params.enable_conda ? 'conda-forge::python=3.11 conda-forge::spectra conda-forge::lzstring conda-forge::imp bioconda::multiqc=1.19' : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' :
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9 'quay.io/biocontainers/multiqc:1.19--pyhdfd78af_0' }"
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10
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11 input:
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12 path pass_and_fail_rel_abn_files
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13 path lineage_csv
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14
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15 output:
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16 path '*.tblsum.txt', emit: mqc_txt, optional: true
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17 path '*_mqc.json' , emit: mqc_json, optional: true
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18 path '*_mqc.yml' , emit: mqc_yml, optional: true
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19 path '*.tsv' , emit: tsv, optional: true
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20 path 'versions.yml', emit: versions
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21
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22 when:
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23 task.ext.when == null || task.ext.when
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24
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25 script:
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26 def args = task.ext.args ?: ''
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27 """
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28 gen_salmon_tph_and_krona_tsv.py \\
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29 $args \\
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30 -sal "." \\
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31 -smres "." \\
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32 -lin $lineage_csv
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33
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34 create_mqc_data_table.py \\
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35 "nowayout" "The results shown here are <code>salmon quant</code> TPM values scaled down by a factor of ${params.gsalkronapy_sf}."
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36
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37 create_mqc_data_table.py \\
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38 "nowayout_indiv_reads_mapped" "The results shown here are the number of reads mapped (post threshold filters) per taxon to the <code>nowayout</code>'s custom <code>${params.db_mode}</code> database for each sample."
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39
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40 cat <<-END_VERSIONS > versions.yml
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41 "${task.process}":
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42 python: \$( python --version | sed 's/Python //g' )
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43 END_VERSIONS
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44 """
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45 } |
