Mercurial > repos > galaxytrakr > hfp_bettercallsal_awsbatch

comparison 1.0.0/modules/bcs_results/main.nf @ 0:801b85b03a17 draft default tip

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planemo upload
author galaxytrakr
date Thu, 28 May 2026 20:31:42 +0000
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-1:000000000000 0:801b85b03a17
1 process BCS_RESULTS {
2 tag "bettercallsal aggregate"
3 label "process_pico"
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
6 conda (params.enable_conda ? "conda-forge::python=3.10 conda-forge::pyyaml" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
9 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
10
11 input:
12 path salmon_res_dirs
13
14 output:
15 path 'bettercallsal*.tblsum.txt', emit: mqc_txt, optional: true
16 path 'bettercallsal*_mqc.json' , emit: mqc_json, optional: true
17 path 'bettercallsal*_mqc.yml' , emit: mqc_yml, optional: true
18 path 'versions.yml' , emit: versions
19
20 when:
21 task.ext.when == null || task.ext.when
22
23 script:
24 def args = task.ext.args ?: ''
25 args += (params.tuspy_ps ? " -pickle ${params.tuspy_ps}" : '')
26 args += (params.gsrpy_snp_clus_metadata ? " -snp ${params.gsrpy_snp_clus_metadata}" : '')
27 """
28 gen_salmon_res_table.py \\
29 $args \\
30 -sal "."
31
32 create_mqc_data_table.py \\
33 "bettercallsal" "The following table is an aggregation of serotype calls from all samples which also includes read counts from <code>salmon quant</code> results."
34
35 create_mqc_data_table.py \\
36 "bettercallsal_salyn" "The following table summarizes serotype presence or absence for all samples."
37
38 cat <<-END_VERSIONS > versions.yml
39 "${task.process}":
40 python: \$( python --version | sed 's/Python //g' )
41 END_VERSIONS
42 """
43 }