Closed jbv2 closed 10 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit b99321c
+| ✅ 156 tests passed |+
!| ❗ 19 tests had warnings |!
@jfy133 The module doesn't have multiqc as outputs (as in DEDUPLICATE), if I added I got an error.
ERROR ~ No such variable: Exception evaluating property 'mqc' for nextflow.script.ChannelOut, Reason: groovy.lang.MissingPropertyException: No such property: mqc for class: groovyx.gpars.dataflow.DataflowBroadcast
That's because the mqc
output channel is from a Subworkflow not a module.
You just need https://multiqc.info/modules/qualimap/ output channel that has the files containing the ones needed by multiQC that you can see here: https://multiqc.info/modules/qualimap/
That's because mqc
is from a Subworkflow not a module.
You just need the output channel that has the files containing the ones needed by multiQC that you can see here: https://multiqc.info/modules/qualimap/
(So basically the results output channel from the module:))
Currently the snpcapture_bed
option is not actually tested in CIs. We can test it once it is added to the reference sheet etc, but does Qualimap successfully run locally when you supply a bed file?
Qualimap ran correctly, providing a BED locally. This might need to be added for testing.
PLease add it to nf-core/test-datasets
eager
branch if one diesn't already exist!
@jbv2 See the unresolved comments about code style and conventions. Please fix the issues and then I think we are good to go! ^_^ 🚀
I approve! GitHub mobile won't let me review again so I will force merge
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).