metaproviz/internalstandard module #12957 - #12958
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ChristinaSchmidt1 wants to merge 14 commits into
Open
ChristinaSchmidt1 wants to merge 14 commits into
ChristinaSchmidt1 wants to merge 14 commits into
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giuliaroeth
requested review from
edmundmiller and
maxulysse
as code owners
September 15, 2026 11:12
…ake the condition column name configurable (was hardcoded to Conditions before)
…nce we use a Dockerfile. Fix spacing issue in Dockerfile
4 tasks
…kerfile and add README.md file that contains information about the shared Image, since we will add more metaproviz modules in the future that will share this image.
…f with the current nf-core module template. meta.yml: added identifier, ontologies, and a top-level versions: block. main.nf: versions.yml now emitted via topic with a tool-specific name (versions_internalstandard), added the conda/mamba guard, trimmed comments.
…tes/. Replaces resources/usr/bin/internal_standard.R + moduleBinaries with templates/internal_standard.R. Inputs are now interpolated directly as R literals instead of parsed from commandArgs().
…s/nextflow.config. Its only content was a docker profile block, which is unnecessary here — the shared tests/config/nf-test.config at the repo root already defines that profile for every module. Deleted the file and the config ./nextflow.config line in tests/main.nf.test that referenced it, matching several other recently-added modules (e.g. openms/mztabexporter) that have no test-specific config at all.
kubranarci
self-requested a review
September 17, 2026 13:19
kubranarci
reviewed
Sep 17, 2026
| tuple val(meta), path("*.plots.rds") , emit: plots | ||
| tuple val(meta), path("*.report.html") , emit: report | ||
| tuple val(meta), path("*.log") , emit: log | ||
| path "versions.yml" , emit: versions_internalstandard, topic: versions |
Contributor
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you can have another line for versions_r_base
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I added that extra line for versions_r_base like you suggested — two topic: versions emits now, one for MetaProViz and one for base R. Is that what you had in mind?
kubranarci
reviewed
Sep 17, 2026
| ${prefix}.condition_cv.tsv ${prefix}.plots.rds \\ | ||
| ${prefix}.report.html ${prefix}.log | ||
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| cat <<-END_VERSIONS > versions.yml |
Contributor
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this can be removed as version is in topic channels
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Sorry, I'm a bit lost on this one. From what I understand, topic channels just expose an already-written versions.yml rather than replace writing it, and the heredoc still seems required for template modules (?)
kubranarci
reviewed
Sep 17, 2026
| description: Sample metadata (TSV/CSV), first column the sample ID matching data_matrix's columns. Required together with data_matrix and feature_matrix if se_rds is not given; pass [] otherwise. | ||
| pattern: "*.{tsv,csv}" | ||
| optional: true | ||
| ontologies: [] |
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ontologies are highly appreciated
kubranarci
reviewed
Sep 17, 2026
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make sure to add snapshot for the test
…osted test data, fix empty-file snapshot lint failure
… versions.yml into two topic emits, versions_metaproviz and versions_r_bas. update tests/main.nf.test assertions and regenerate the snapshots.
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PR checklist
Closes #XXX
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