Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.5.0/modules/bcs_results/main.nf @ 1:365849f031fd
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 05 Jun 2023 18:48:51 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@1 | 1 process BCS_RESULTS { |
| kkonganti@1 | 2 tag "bettercallsal aggregate" |
| kkonganti@1 | 3 label "process_pico" |
| kkonganti@1 | 4 |
| kkonganti@1 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) |
| kkonganti@1 | 6 conda (params.enable_conda ? "conda-forge::python=3.10 conda-forge::pyyaml" : null) |
| kkonganti@1 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@1 | 8 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : |
| kkonganti@1 | 9 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" |
| kkonganti@1 | 10 |
| kkonganti@1 | 11 input: |
| kkonganti@1 | 12 path salmon_res_dirs |
| kkonganti@1 | 13 |
| kkonganti@1 | 14 output: |
| kkonganti@1 | 15 path 'bettercallsal*.tblsum.txt', emit: mqc_txt, optional: true |
| kkonganti@1 | 16 path 'bettercallsal*_mqc.json' , emit: mqc_json, optional: true |
| kkonganti@1 | 17 path 'bettercallsal*_mqc.yml' , emit: mqc_yml, optional: true |
| kkonganti@1 | 18 path 'versions.yml' , emit: versions |
| kkonganti@1 | 19 |
| kkonganti@1 | 20 when: |
| kkonganti@1 | 21 task.ext.when == null || task.ext.when |
| kkonganti@1 | 22 |
| kkonganti@1 | 23 script: |
| kkonganti@1 | 24 def args = task.ext.args ?: '' |
| kkonganti@1 | 25 args += (params.tuspy_ps ? " -pickle ${params.tuspy_ps}" : '') |
| kkonganti@1 | 26 args += (params.gsrpy_snp_clus_metadata ? " -snp ${params.gsrpy_snp_clus_metadata}" : '') |
| kkonganti@1 | 27 """ |
| kkonganti@1 | 28 gen_salmon_res_table.py \\ |
| kkonganti@1 | 29 $args \\ |
| kkonganti@1 | 30 -sal "." |
| kkonganti@1 | 31 |
| kkonganti@1 | 32 create_mqc_data_table.py \\ |
| kkonganti@1 | 33 "bettercallsal" "The following table is an aggregation of serotype calls from all samples which also includes read counts from <code>salmon quant</code> results." |
| kkonganti@1 | 34 |
| kkonganti@1 | 35 create_mqc_data_table.py \\ |
| kkonganti@1 | 36 "bettercallsal_salyn" "The following table summarizes serotype presence or absence for all samples." |
| kkonganti@1 | 37 |
| kkonganti@1 | 38 cat <<-END_VERSIONS > versions.yml |
| kkonganti@1 | 39 "${task.process}": |
| kkonganti@1 | 40 python: \$( python --version | sed 's/Python //g' ) |
| kkonganti@1 | 41 END_VERSIONS |
| kkonganti@1 | 42 """ |
| kkonganti@1 | 43 } |