Closed TCLamnidis closed 1 year ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 1abd118
+| ✅ 158 tests passed |+
!| ❗ 19 tests had warnings |!
Agreed that we should stick to
tag
be for HOST_REMOVAL
? Also, how will that work with multiple references? 😬 LGTM!
Still pending (potentially):
Updates:
meta.id
calls tometa.sample_id
calls.${meta.id}
to${meta.sample_id}_${meta.library_id}_L${meta.lane}
(lane only when it applies).meta.genomic_region
to process tags for deduplication as${meta.reference}:${meta.genomic_region}
This PR also enforces some formatting changes to the
modules.conf
, that will be required from now on:SAMTOOLS_*
) MUST be given unique informative names, to avoid configuration "leakage" into unintended parts of the pipeline.meta.id
as a tag/prefix if possible. Use the minimal unique combination ofmeta.sample_id
,meta.library_id
andmeta.lane
instead.PR checklist
scrape_software_versions.py
nf-core lint .
).nextflow run . -profile test,docker
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).