Add ViralConsensus module #9655
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SPPearce
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SPPearce
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Can you take a look at:
https://nf-co.re/docs/guidelines/components/modules#configuration-of-extargs-in-tests
and configure the ext.args that way please.
Or if they are all the same after you change the ext., then I guess just have the one nextflow.config
| { assert process.out.fasta }, | ||
| { assert process.out.pos_counts }, | ||
| { assert process.out.ins_counts }, | ||
| { assert snapshot(process.out.versions_viralconsensus).match("optional_versions") } |
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Are none of these files stable and able to be put into the snapshot?
| { assert snapshot( | ||
| process.out.fasta, | ||
| process.out.findAll { key, val -> key.startsWith("versions") } | ||
| ).match() } |
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This could probably just be
| { assert snapshot( | |
| process.out.fasta, | |
| process.out.findAll { key, val -> key.startsWith("versions") } | |
| ).match() } | |
| { assert snapshot(process.out.fasta).match() } |
i.e. you are just testing everything that is generated.
Same applies to the others too by the looks of it.
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| input: | ||
| tuple val(meta), path(bam) | ||
| path fasta |
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We generally add a meta map to the fasta, to help for pipelines that want to consider multiple genomes.
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Thanks @SPPearce for the review(s). The latest changes are addressed, at the cost of passing linting (at least based on |
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out.fasta).match() } |
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Apologies, this should have been
| { assert snapshot(process.out.fasta).match() } | |
| { assert snapshot(process.out).match() } |
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out.fasta).match() } |
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| { assert snapshot(process.out.fasta).match() } | |
| { assert snapshot(process.out).match() } |
| [ | ||
| "VIRALCONSENSUS", | ||
| "viralconsensus", | ||
| "viral_consensus v1.0.0" |
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This isn't being trimmed properly, should just be 1.0.0 here.
| tuple val(meta), path("*.consensus.fa"), emit: fasta | ||
| tuple val(meta), path("*.pos_counts.tsv"), optional: true, emit: pos_counts | ||
| tuple val(meta), path("*.ins_counts.json"), optional: true, emit: ins_counts | ||
| tuple val("${task.process}"), val('viralconsensus'), eval("viral_consensus --version 2>&1 | head -n1 | sed 's/ViralConsensus //'"), topic: versions, emit: versions_viralconsensus |
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Can you simplify this command, combining the sed and head. AI is very good at this.
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PR checklist
Closes #9653
This PR adds ViralConsensus as an nf-core/module.
topic: versions- See version_topicslabelnf-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