feat!(PCGR): move sample params to samplesheet#96
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add sample params to subMap so they are not filtered out
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famosab
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It looks good to me, I just have one question regarding validation of the samplesheet and handling of germline-only runs :)
for samples with status: 0 (germline) columns like tumor_site have no biological meaning and should hence be rejected.
…lues default values for optional sample-params are defined in input schema only. They not necessarily included in the tool call. PCGR will handle its default behaviour. This change intends to prevent diversion in defaults between pipeline and pcgr in the future.
these empty dirs/files serve as dummys for tests, where the pipeline should think the reference data is present without actually using it. This can prevent the test from downloading the reference data for that test.
famosab
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Jul 6, 2026
famosab
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Jul 6, 2026
test optional columns for somatic rows in one single test, each invalid field will throw an error
multiple warning ignore declarations otherwise overwrite each other. you can now specify multiple warnings to ignore as an array
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Hm maybe we can put this into test-datasets and not have it in the pipeline directly?
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hm yes that sounds good. then I'll move the samplesheets to the test-datasets aswell?
nf-core/test-datasets#2137
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add samplesheets and dummy reference data for tests introduced in nf-core/variantprioritization#96
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this PR moves sample-specific parameters for PCGR to the samplesheet.
Params moved:
tumor_sitetumor_puritytumor_ploidyThis is a breaking, backwards-incompatible change, as the moved params are no longer supported as pipeline parameters (via CLI or params file).
closes #87
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).