Move reference preparation to main.nf#754
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ramprasadn merged 14 commits intodevfrom Dec 11, 2025
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@nf-core-bot fix linting |
fellen31
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Nice with more tested tools 🚀
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| skip_tools = 'fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse,ngsbits' | ||
| skip_subworkflows = "mt_annotation,mt_subsample,sv_annotation" |
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| include { CREATE_HGNCIDS_FILE } from './modules/local/create_hgncids_file' | ||
| include { CREATE_PEDIGREE_FILE } from './modules/local/create_pedigree_file' | ||
| include { parseSkipList } from './subworkflows/local/utils_nfcore_raredisease_pipeline' | ||
| include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_raredisease_pipeline' | ||
| include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_raredisease_pipeline' | ||
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| include { PREPARE_REFERENCES } from './subworkflows/local/prepare_references' | ||
| include { RAREDISEASE } from './workflows/raredisease' | ||
| include { SCATTER_GENOME } from './subworkflows/local/scatter_genome' |
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Why did you decide on moving these subworkflows here?
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I decided to move them here for two reasons:
- These steps relate to reference files, not the actual analysis, so it makes logical sense to keep them outside the main analysis flow.
- When I eventually create a “download references” workflow, it will be easier to connect it with “prepare references” if these steps are kept separate.
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| skip_eklipse = parseSkipList(params.skip_tools, 'eklipse') | ||
| skip_fastp = parseSkipList(params.skip_tools, 'fastp') | ||
| skip_fastqc = parseSkipList(params.skip_tools, 'fastqc') | ||
| skip_gens = parseSkipList(params.skip_tools, 'gens') | ||
| skip_germlinecnvcaller = parseSkipList(params.skip_tools, 'germlinecnvcaller') | ||
| skip_haplogrep3 = parseSkipList(params.skip_tools, 'haplogrep3') | ||
| skip_ngsbits = parseSkipList(params.skip_tools, 'ngsbits') | ||
| skip_peddy = parseSkipList(params.skip_tools, 'peddy') | ||
| skip_qualimap = parseSkipList(params.skip_tools, 'qualimap') | ||
| skip_smncopynumbercaller = parseSkipList(params.skip_tools, 'smncopynumbercaller') | ||
| skip_vcf2cytosure = parseSkipList(params.skip_tools, 'vcf2cytosure') |
fellen31
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Bit hard to review with so many parts moving, but snapshots and everything else looks good so looks fine to me!
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Tack tack! |
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PR checklist
This PR moves reference generation from raredisease.nf to main.nf.
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile test_singleton,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).