Pre-release dev branch #151
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Co-authored-by: Evangelos Karatzas <[email protected]>
Co-authored-by: Evangelos Karatzas <[email protected]>
Co-authored-by: Evangelos Karatzas <[email protected]>
Co-authored-by: Evangelos Karatzas <[email protected]>
Co-authored-by: Evangelos Karatzas <[email protected]>
Co-authored-by: Evangelos Karatzas <[email protected]>
Co-authored-by: Evangelos Karatzas <[email protected]>
Co-authored-by: Evangelos Karatzas <[email protected]>
Co-authored-by: Evangelos Karatzas <[email protected]>
Co-authored-by: Evangelos Karatzas <[email protected]>
vagkaratzas
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Sep 11, 2025
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Alright, tons of work and getting there!
I've left some comments, and now the tests need to pass, and will definitely catch more errors on the dev -> main PR to fix. Just an additional comment for the future; try to slowly convert local modules and subworkflows to nf-core style --adding metas, versions, meta.yml, tests etc
vagkaratzas
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Sep 12, 2025
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vagkaratzas
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Almost there, just remove the .nf-test.log file and run prettier -w on the formatting failed paths from the error.
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PR checklist
nf-core lint .).nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).Pipeline completes successfully using test data with the following command:
nextflow run main.nf -profile test,dockernf-core subworkflow moved to local:
bam_variant_calling_sort_freebayes (FreeBayes module updated but not subworkflow - slack thread)
nf-core modules moved to local:
bcftools consensus (step to exclude indels from vcf with bcftools view added and additional bcftools index command to index new vcf file)
clair3 (incorrect flag. Module has --model, should be --model_path)
bedtools genomecov (module simplified compared to nf-core version to make life a little easier)
rasusa (genome_size moved to a separate input not same tuple as meta/reads to make life a little easier)