Closed TCLamnidis closed 1 year ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit fcee8af
+| ✅ 157 tests passed |+
!| ❗ 18 tests had warnings |!
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Merge away @TCLamnidis then look at my PR :laughing:
This adds the
deduplicate
subworkflow. This subworkflow:picard MarkDuplicates
(the default), ordedup
to do thissamtools flagstat
This approach should be a lot faster (since it is more parallelised) and require a smaller amount of resources to run.
Additionally, this PR updated the MAP subworkflow to perform lane-wise merging and provide a sorted, indexed, flagstatted bamfile.
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).