Closed RobJY closed 2 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 2ce3d07
+| ✅ 165 tests passed |+
#| ❔ 1 tests were ignored |#
!| ❗ 28 tests had warnings |!
Question. If I understood correctly these changes allow two formatting options for the sample sheet right?, one is the cycle per row per sample using the "image_tiles" column and the second option is sample per row using the" image_directory" column. The first option points to the cycle_xxx.tif, while the second to the directory with the .tif of all cycles?
Yes, you can see example samplesheets for both cases in the assets directory that are used for the nf-tests in tests/main.nf.test
I think that the testing is a bit messy regarding which are the inputs and the outputs, and what is being tested. And yeah the workflow sections have to be filled out and tests run.
The tests can probably be refactored now that the workflow inputs are more logical with the new template layout. I will have a better idea about that by the end of the week when I finish that refactor/merge.
Amazing work @jmuhlich, LGTM, nice and clean.
Sorry to pull the rug out from folks who have reviewed, but after I started making substantial updates to this branch it got rather out of date with Rob's original version and we decided it would be best to create a new PR. So I'm closing this in favor of #29.
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).