Adding cnaqc tool module #8890
Adding cnaqc tool module #8890
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| process CNAQC { | |||
| tag "$meta.id" | |||
| label 'process_low' | |||
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Does your script allow multi-threading? If no then change to process_single :)
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| process CNAQC { | |||
| tag "$meta.id" | |||
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| tag "$meta.id" | |
| tag "${meta.id}" |
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| output: | ||
| tuple val(meta), path("*_qc.rds"), emit: qc_rds | ||
| tuple val(meta), path("*_data_plot.rds"), path("*_qc_plot.rds"), emit: plot_rds |
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Can you adjust this to have only one file per output channel?
| stub: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
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| licence: ["GPL v3-or-later"] | ||
| identifier: "" | ||
| input: | ||
| # Only when we have meta |
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| # Only when we have meta |
| type: file | ||
| description: R object with mutation data | ||
| pattern: "*.rds" | ||
| ontologies: [] |
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Can you look for ontologies please?
| ext.args = [ | ||
| genome : "GRCh38", | ||
| matching_strategy : "rightmost", | ||
| purity_error : "0.05", | ||
| muts_per_karyotype : "25", | ||
| min_absolute_karyotype_mutations : "100" |
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Are these necessary arguments for the tool to be able to run? If yes they need to be reflected in the module definition as value input channels for example :)
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I am not an expert on R so maybe someone else needs to be asked to review this part!
| { assert snapshot( | ||
| process.out.versions | ||
| ).match() }, | ||
| // Check nondeterministic files exist | ||
| { assert file(process.out.qc_rds[0][1]).exists() }, | ||
| { assert file(process.out.plot_rds[0][1]).exists() }, | ||
| { assert file(process.out.plot_pdf_data[0][1]).exists() }, | ||
| { assert file(process.out.plot_pdf_qc[0][1]).exists() } |
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Can we add more stuff to the snapshot? Maybe at least get the name of each file that is in th eoutput and append that to the snap?
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } |
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Can you add path(process.out.versions[0]).yaml to check whether the version is accessed correctly?
PR checklist
Closes #8610
Reopening the PR with a clean state as asked in #8714 (comment)
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda