Closed tillenglert closed 1 year ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit dbdc4fd
+| ✅ 159 tests passed |+
!| ❗ 12 tests had warnings |!
Should I already add parameters for the tool versions? Only one tool at a time is allowed right now right, so it wouldn't be that hard. But still I would need some hardcoding to access all possible tools and versions as far as I can think atm.
@nf-core-bot fix linting
The corresponding test_model_information will fail, due to the missing docker registry (will be fixed when merging template update 2.8).
I added a check for the requested allele model corresponding to the tool which is used. The check is performed during the
samplesheet_check
. (The input check module will be renamed and restructured in a following structure and cleanup PR)Moreover I added a functionality to let the user output all supported models for each tool as a help function. It can be called by e.g.
nextflow run nf-core/metapep -profile docker --outdir <OUTDIR> --show_supported_models
. Adding this functionality needed to add a groovy function to check if the--input
is required or the--show_supported_models
is set.The versions of the prediction methods are extracted from the used container/epytope version.
Solves issue: #48
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).