Release 3.4.1 #1460
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Release 3.4.1 #1460
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…cs and cnvkit/reference
Update mulled-containers to samtools v1.19.2
Where is Edmund?
Important! Template update for nf-core/tools v2.13
Fix test name
Clean up code changes
feat(modules): update vep to 111.0
Fixing sentieon - code and tests
Multiqc channels
fix(schema): add some params to validationSchemaIgnoreParams for better handling
fix(vep_cache_version-snpeff_db): both params are string
kenibrewer
reviewed
Apr 19, 2024
| case 'variant_calling': log.warn("Using file ${outdir}/csv/recalibrated.csv"); | ||
| input = outdir + "/csv/recalibrated.csv" | ||
| break | ||
| // case 'controlfreec': csv_file = file("${outdir}/variant_calling/csv/control-freec_mpileup.csv", checkIfExists: true); break |
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Is this commented out section intended to be used in a future feature? Otherwise we may wish to delete it.
Suggested change
| // case 'controlfreec': csv_file = file("${outdir}/variant_calling/csv/control-freec_mpileup.csv", checkIfExists: true); break |
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It's a past feature that we want to restore at some point, good spot
fix(spark): load spark profile after loading the test profiles
|
All missing md5sum are from pytest tests that we decided to slowly depreciate and as md5sum are way more complicated to update, if there's any issue, we don't update anymore until we move to nf-test |
kenibrewer
approved these changes
Apr 19, 2024
svarona
reviewed
Apr 22, 2024
svarona
approved these changes
Apr 22, 2024
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PR checklist
nf-core lint).nextflow run . -profile 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).