Add ViralConsensus module #9655
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SPPearce
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Jan 21, 2026
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| def pos_counts_arg = task.ext.save_pos_counts ? "-op ${prefix}.pos_counts.tsv" : '' | ||
| def ins_counts_arg = task.ext.save_ins_counts ? "-oi ${prefix}.ins_counts.json" : '' |
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We don't like adding new task.ext values. Can these be optional inputs instead please.
SPPearce
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Jan 21, 2026
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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 snapshot( | ||
| process.out.fasta, | ||
| process.out.versions_viralconsensus | ||
| ).match("basic") } |
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| ).match("basic") } | |
| ).match() } |
| { assert snapshot( | ||
| process.out.fasta, | ||
| process.out.versions_viralconsensus | ||
| ).match("primer") } |
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| ).match("primer") } | |
| ).match() } |
| { 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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| { assert snapshot(process.out.versions_viralconsensus).match("optional_versions") } | |
| { assert snapshot(process.out.versions_viralconsensus).match() } |
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match("stub") } |
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| { assert snapshot(process.out).match("stub") } | |
| { assert snapshot(process.out).match() } |
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| { 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?
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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