Closed LilyAnderssonLee closed 12 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 484c392
+| ✅ 156 tests passed |+
!| ❗ 2 tests had warnings |!
@sofstam, thanks for reporting this issue. It's curious because I recall that we had addressed the input for 'centrifuge_report' before. It's possible that we overlooked it when incorporating it into 'combineProfilesWithDatabase' at a later stage."
I have tested it, and it worked quite well.
I swear we had fixed this but OK!
I swear we had fixed this but OK!
I thought so as well. However, now we are very certain that it has been fixed.
In profiling.nf, correct the input for
CENTRIFUGE_KREPORT
to specify theresults
file rather than thereport
file.The output of centrifuge_kreport when using the report file (old code): The assgined reads counts are not correct
The output of centrifuge_kreport when using the results file (corrected one):
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).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).