Add association and heritability analysis routes - #99
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 4.0.3. For more documentation on how to update your pipeline, please see the Synchronisation documentation. |
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chriswyatt1
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| @@ -26,36 +25,36 @@ process { | |||
| // adding in your local modules too. | |||
| // TODO nf-core: Customise requirements for specific processes. | |||
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| // TODO nf-core: Customise requirements for specific processes. |
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Maybe in the template, but I think theres normally info here,
// Process-specific resource requirements
// NOTE - Please try and reuse the labels below as much as possible.
// These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
// If possible, it would be nice to keep the same label naming convention when
// adding in your local modules too.
// See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
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@lyh970817 . Hey, I will try to finish the review on this by next week. Looks great though, what I have gone through so far |
# Conflicts: # README.md # docs/usage.md # nextflow_schema.json # ro-crate-metadata.json # subworkflows/local/utils_nfcore_gwas_pipeline/main.nf # subworkflows/local/validate_gwas_input/main.nf # subworkflows/local/validate_gwas_input/tests/main.function.nf.test # tests/full_scale.nf.test # tests/full_scale.nf.test.snap
# Conflicts: # docs/usage.md # ro-crate-metadata.json # subworkflows/local/validate_gwas_input/main.nf # workflows/gwas.nf
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Description
This PR replaces the existing
--inputsamplesheet contract ondevwith linked cohort and analysis manifests, then wires the association and individual-level heritability routes that consume that relational model.Compared with
dev, this PR:--cohort_manifest,--analysis_manifestand optional--method_optionsinputs with dedicated schemas and validation;The usage, output, README, citations and development changelog documentation are updated for the submitted interface and routes.
Important
This draft must not be merged until nf-core/test-datasets#2198 has been merged into the
gwasbranch. The test profiles in this PR intentionally reference those canonical fixture URLs.Companion fixture PR: nf-core/test-datasets#2198
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).