Feature/prs modules - #10
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Feature/modules test
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Feature/variant calling prs
Feature/prs modules
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rernst
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rernst
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Looks good, some minor remarks / discussion points and comments:
- Add version to (python) tools instead of nextflow module.
- Update diff comparisons to reflect update modules -> maybe evaluate whether we still need to 'copy' these nf-core modules in our own repo (out of scope for this PR)?
- I think it would be a good idea to create a separate 'prsutils' repo for the python tools in that module. Comparable to what we want to do with for example DIMS.
| # Required for nft-utils nfcoreInstall() to install nf-core modules | ||
| # during test setup (provides the `nf-core` CLI on PATH). | ||
| shell: bash | ||
| run: python -m pip install --upgrade --force-reinstall git+https://github.com/UMCUGenetics/nf-core-tools.git |
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Do we still need our own checkout -> if so, we should make sure to keep it up to date.
| output: | ||
| tuple val(meta), path("*_knn.tsv"), emit: knn_tsv | ||
| tuple val(meta), path("*_knn_pca.png"), emit: knn_pca_plot, optional: true | ||
| tuple val("${task.process}"), val('ancestry_knn'), eval('echo 1.0.0'), emit: versions_ancestry_knn, topic: versions |
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I think we should add a version to the script -> instead of hardcoding it in the nextflow module.
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Why do we need our own custom GATK module? Do we use a different version?
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Should we add a meta.yml for our modules as well? Is there any added value?
| -o ${prefix}_normalised.txt.gz | ||
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| echo "pgscatalog-combine: 1.4.4" > versions.yml |
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I think this file should als be updated to reflect latest differences?
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I think this file should als be updated to reflect latest differences?
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I think this file should als be updated to reflect latest differences?
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| main: | ||
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| // [model_meta, snplist, vcf, tbi] |
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Is this a comment reflecting the structure of ch_snp_vcf?
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The modules and subworkflows from DxNextflowPRS have been moved to the central Modules repository. A few small refactors have been made to make the subworkflows more 'stand alone', but 90% of the content of this PR was previously reviewed and is already used in production (https://github.com/UMCUGenetics/DxNextflowPRS/tree/main)