Closed asp8200 closed 3 months ago
nf-core lint
overall result: Failed :x:Posted for pipeline commit 7b7e031
+| ✅ 189 tests passed |+
#| ❔ 1 tests were ignored |#
!| ❗ 5 tests had warnings |!
-| ❌ 2 tests failed |-
Version 2.14.1
of the nf-core/tools pipeline template has just been released. This pull-request is now outdated and has been closed in favour of https://github.com/nf-core/bamtofastq/pull/91
Please use https://github.com/nf-core/bamtofastq/pull/91 to merge in the new changes from the nf-core template as soon as possible.
@maxulysse : Anything else I should do as part of "back to dev"?
so this one replaces https://github.com/nf-core/bamtofastq/pull/89?
@mirpedrol : As you can see, I did add both fasta and fasta_fai to validationSchemaIgnoreParams so why do I get that warning about fasta being uninitialised?
I am unsure what is causing this, it could be a bug on nf-schema, we see the same behaviour with monochromeLogs
. I will need more time to look into this. But it shouldn't affect the correct running of your pipeline.
Currently, getting
" WARN: Access to undefined parameter
fasta
-- Initialise it to a default value eg.params.fasta = some_value
WARN: Access to undefined parametermonochromeLogs
-- Initialise it to a default value eg.params.monochromeLogs = some_value
"@mirpedrol : As you can see, I did add both
fasta
andfasta_fai
tovalidationSchemaIgnoreParams
so why do I get that warning aboutfasta
being uninitialised?PR checklist
nf-core lint
).nf-test test main.nf.test -profile test,docker
).nextflow run . -profile debug,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).