Closed taylorreiter closed 1 year ago
master
branch :x:base
to dev
Hi @taylorreiter,
It looks like this pull-request is has been made against the Arcadia-Science/seqqc master
branch.
The master
branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master
are only allowed if they come from the Arcadia-Science/seqqc dev
branch.
You do not need to close this PR, you can change the target branch to dev
by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.
Thanks again for your contribution!
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit c2e6132
+| ✅ 125 tests passed |+
#| ❔ 20 tests were ignored |#
!| ❗ 5 tests had warnings |!
This PR introduces a new test data set: https://github.com/Arcadia-Science/test-datasets/blob/main/seqqc/samplesheet_test.csv
For now, it only swaps out the small test data set. I might swap the large one later, but I want to think about it a bit more before I do that.
This PR also fixes a small bug I found that caused the gather results to not be passed to the pubDir, which caused the gather results not to be included in the multiqc html. i didn't catch it with the old test data set because that data set didn't produce any gather results, so it was normal for it to be missing.
Lastly, I also removed an annoying exit from the samplesheet check file. The lines inappropriately caused nextflow to fail saying that the samplesheet didn't have a header, but it certainly had a header. This has happened to me on three separate occasions so I felt like it was making the code unnecessarily brittle.
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).