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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
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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 |
| 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 | sed 's/.*v//'"), topic: versions, emit: versions_viralconsensus |
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Have you checked if the 2>&1 is required? Depends on whether the tool writes to stdout or stderr.
SPPearce
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Can you just check if it works without the 2>&1, but otherwise looks good.
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@SPPearce Sorry for the history rewrite but I've completed your request. No difference as far as I can tell. |
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@lucaspatel , you should ask on the nf-core Slack channel to join the organisation, so the tests run for you. |
* feat: Added ViralConsensus module * fix: update test snapshots for Docker compatibility * fix: task.ext to optional inputs * fix: update configuration of ext.args in tests * fix: simplify test asserts, though breaks linting * fix: add meta map to fasta input * fix: tests match and sed/head handling * chore: remove shell redirect
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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