Mercurial > repos > kkonganti > hfp_nowayout
annotate 0.5.0/modules/nowayout_results/main.nf @ 0:97cd2f532efe
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 31 Mar 2025 14:50:40 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@0 | 1 process NOWAYOUT_RESULTS { |
| kkonganti@0 | 2 tag "nowayout aggregate" |
| kkonganti@0 | 3 label "process_pico" |
| kkonganti@0 | 4 |
| kkonganti@0 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) |
| kkonganti@0 | 6 conda (params.enable_conda ? 'conda-forge::python=3.11 conda-forge::spectra conda-forge::lzstring conda-forge::imp bioconda::multiqc=1.19' : null) |
| kkonganti@0 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@0 | 8 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : |
| kkonganti@0 | 9 'quay.io/biocontainers/multiqc:1.19--pyhdfd78af_0' }" |
| kkonganti@0 | 10 |
| kkonganti@0 | 11 input: |
| kkonganti@0 | 12 path pass_and_fail_rel_abn_files |
| kkonganti@0 | 13 path lineage_csv |
| kkonganti@0 | 14 |
| kkonganti@0 | 15 output: |
| kkonganti@0 | 16 path '*.tblsum.txt', emit: mqc_txt, optional: true |
| kkonganti@0 | 17 path '*_mqc.json' , emit: mqc_json, optional: true |
| kkonganti@0 | 18 path '*_mqc.yml' , emit: mqc_yml, optional: true |
| kkonganti@0 | 19 path '*.tsv' , emit: tsv, optional: true |
| kkonganti@0 | 20 path 'versions.yml', emit: versions |
| kkonganti@0 | 21 |
| kkonganti@0 | 22 when: |
| kkonganti@0 | 23 task.ext.when == null || task.ext.when |
| kkonganti@0 | 24 |
| kkonganti@0 | 25 script: |
| kkonganti@0 | 26 def args = task.ext.args ?: '' |
| kkonganti@0 | 27 """ |
| kkonganti@0 | 28 gen_salmon_tph_and_krona_tsv.py \\ |
| kkonganti@0 | 29 $args \\ |
| kkonganti@0 | 30 -sal "." \\ |
| kkonganti@0 | 31 -smres "." \\ |
| kkonganti@0 | 32 -lin $lineage_csv |
| kkonganti@0 | 33 |
| kkonganti@0 | 34 create_mqc_data_table.py \\ |
| kkonganti@0 | 35 "nowayout" "The results shown here are <code>salmon quant</code> TPM values scaled down by a factor of ${params.gsalkronapy_sf}." |
| kkonganti@0 | 36 |
| kkonganti@0 | 37 create_mqc_data_table.py \\ |
| kkonganti@0 | 38 "nowayout_indiv_reads_mapped" "The results shown here are the number of reads mapped (post threshold filters) per taxon to the <code>nowayout</code>'s custom <code>${params.db_mode}</code> database for each sample." |
| kkonganti@0 | 39 |
| kkonganti@0 | 40 cat <<-END_VERSIONS > versions.yml |
| kkonganti@0 | 41 "${task.process}": |
| kkonganti@0 | 42 python: \$( python --version | sed 's/Python //g' ) |
| kkonganti@0 | 43 END_VERSIONS |
| kkonganti@0 | 44 """ |
| kkonganti@0 | 45 } |