Mercurial > repos > galaxytrakr > hfp_nowayout_awsbatch

comparison 0.5.0/modules/nowayout_results/main.nf @ 0:3c767f9cfd88 draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:37:56 +0000
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-1:000000000000 0:3c767f9cfd88
1 process NOWAYOUT_RESULTS {
2 tag "nowayout aggregate"
3 label "process_pico"
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
6 conda (params.enable_conda ? 'conda-forge::python=3.11 conda-forge::spectra conda-forge::lzstring conda-forge::imp bioconda::multiqc=1.19' : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' :
9 'quay.io/biocontainers/multiqc:1.19--pyhdfd78af_0' }"
10
11 input:
12 path pass_and_fail_rel_abn_files
13 path lineage_csv
14
15 output:
16 path '*.tblsum.txt', emit: mqc_txt, optional: true
17 path '*_mqc.json' , emit: mqc_json, optional: true
18 path '*_mqc.yml' , emit: mqc_yml, optional: true
19 path '*.tsv' , emit: tsv, optional: true
20 path 'versions.yml', emit: versions
21
22 when:
23 task.ext.when == null || task.ext.when
24
25 script:
26 def args = task.ext.args ?: ''
27 """
28 gen_salmon_tph_and_krona_tsv.py \\
29 $args \\
30 -sal "." \\
31 -smres "." \\
32 -lin $lineage_csv
33
34 create_mqc_data_table.py \\
35 "nowayout" "The results shown here are <code>salmon quant</code> TPM values scaled down by a factor of ${params.gsalkronapy_sf}."
36
37 create_mqc_data_table.py \\
38 "nowayout_indiv_reads_mapped" "The results shown here are the number of reads mapped (post threshold filters) per taxon to the <code>nowayout</code>'s custom <code>${params.db_mode}</code> database for each sample."
39
40 cat <<-END_VERSIONS > versions.yml
41 "${task.process}":
42 python: \$( python --version | sed 's/Python //g' )
43 END_VERSIONS
44 """
45 }