Closed fa2k closed 4 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 9465bc8
+| ✅ 182 tests passed |+
#| ❔ 7 tests were ignored |#
!| ❗ 1 tests had warnings |!
Could you sync your changes with the latest dev @fa2k ? Hopefully, that will fix the lint error.
@ramprasadn This seems to have worked :)
This PR solves a problem (#544 ), that not all alleles at a multiallelic indel site get a CADD score. The issue is that all indels aren't selected by
bcftools view .... --types indels
even though they are indels. Only the first indel at a position is selected by bcftools view and therefore scored. The PR includes the "other" variant type in the selection of variants for CADD. It doesn't seem to include a large number of additional variants, so I don't think it will slow down the pipeline significantly.PR checklist
nf-core lint
). There are warnings & errors, but they seem unrelated.nextflow run . -profile test,docker --outdir <OUTDIR>
). CADD is disabled in these tests. I've run a test on a bigger dataset.nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>
). Fails in GENMOD, seems unrelated.nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated. (Will be updated after I get the pull request link)README.md
is updated (including new tool citations and authors/contributors).