Closed DLBPointon closed 10 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit bf90f0e
+| ✅ 126 tests passed |+
#| ❔ 17 tests were ignored |#
!| ❗ 8 tests had warnings |!
Pipeline fails as it needs Pretext_hires to be emitted from hic_mapping but can't as pretext_hires needs 16GB minimum
PR is practically done. Made up of two PR's - pretext_ingestion and better_docs.
Includes re-write of pretext-graph subworkflow from the main treeval level workflow into hic_mapping. This makes it much easier to control when and where the hires versions run.
I just need to update the pictures in the docs and done.
This PR has grown a bit, so to summarise:
Pretext Ingestion!
The accessory files are now ingested into the pretext file, rather than needing the end user to ingest them independently. coverage, log2 coverage and repeat density are ingested by default and telomere + gap are ingested if they contain > 0 bytes.
This highlighted a small bug with the new log_coverage track, which has been corrected with a
round(value, 2)
ensuring that there will always be a whole number for ingestion and no data is skipped.