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1 process BCS_RESULTS {
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2 tag "bettercallsal 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${params.fs}3.8.1" : null)
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6 conda (params.enable_conda ? "conda-forge::python=3.10 conda-forge::pyyaml" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
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9 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
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10
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11 input:
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12 path salmon_res_dirs
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13
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14 output:
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15 path 'bettercallsal*.tblsum.txt', emit: mqc_txt, optional: true
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16 path 'bettercallsal*_mqc.json' , emit: mqc_json, optional: true
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17 path 'bettercallsal*_mqc.yml' , emit: mqc_yml, optional: true
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18 path 'versions.yml' , emit: versions
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19
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20 when:
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21 task.ext.when == null || task.ext.when
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22
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23 script:
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24 def args = task.ext.args ?: ''
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25 args += (params.tuspy_ps ? " -pickle ${params.tuspy_ps}" : '')
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26 args += (params.gsrpy_snp_clus_metadata ? " -snp ${params.gsrpy_snp_clus_metadata}" : '')
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27 """
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28 gen_salmon_res_table.py \\
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29 $args \\
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30 -sal "."
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31
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32 create_mqc_data_table.py \\
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33 "bettercallsal" "The following table is an aggregation of serotype calls from all samples which also includes read counts from <code>salmon quant</code> results."
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34
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35 create_mqc_data_table.py \\
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36 "bettercallsal_salyn" "The following table summarizes serotype presence or absence for all samples."
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37
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38 cat <<-END_VERSIONS > versions.yml
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39 "${task.process}":
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40 python: \$( python --version | sed 's/Python //g' )
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41 END_VERSIONS
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42 """
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43 } |
