Open CarsonJM opened 4 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 5619352
+| ✅ 307 tests passed |+
#| ❔ 2 tests were ignored |#
!| ❗ 5 tests had warnings |!
Not knowing much (yet) about nf-test - I think this looks great!
I had a poke around in the failing tests - here, the kreport test fails because the test reads the mag conf/modules.conf
and sets the prefix as ext.prefix = { "${meta.id}_kreport" }
, whereas the test snapshot expects the output file to just be called ${meta.id}.txt
. I suspect this could be a problem for any test where we're manually setting a prefix and adding custom strings to it which aren't hard-coded in the process itself. Off the top of my head this may cause problems with the read QC filtering, phiX removal, etc. as these add prefixes like "_host_removed" to separate out fastq files which otherwise would have the same names.
Thanks for taking a look at this @prototaxites! I'll look at the module configs today and see which ones need to be changed, I think this is something we can override in an nf-test config 👌
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).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).