Closed grst closed 1 month ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 2e954ef
+| ✅ 187 tests passed |+
#| ❔ 3 tests were ignored |#
!| ❗ 7 tests had warnings |!
@nf-core-bot fix linting
currently doesn't work on S3
currently doesn't work on S3
never mind, it was just an encoding issue in the samplesheet
This will fall apart as soon as we have more than one flowcells with the same samplesheet filenames. This creates a file in the current directory and potentially overwrite each other. I think the correct pattern to use here would be collectFile.
@nschcolnicov, any chance you could look into that?
This will fall apart as soon as we have more than one flowcells with the same samplesheet filenames. This creates a file in the current directory and potentially overwrite each other. I think the correct pattern to use here would be collectFile.
@nschcolnicov, any chance you could look into that?
Absolutely, let me address it in this PR.
Is this ready for review? Looks ready to me :)
I think this looks good, thanks @nschcolnicov! Could we have a test case that ensures that the lines are actually removed? Speaking of experience from an internal pipeline where we thought it would remove those lines but didn't for at least three years.
Is this ready for review? Looks ready to me :)
Yes, thank you!
I think this looks good, thanks @nschcolnicov! Could we have a test case that ensures that the lines are actually removed? Speaking of experience from an internal pipeline where we thought it would remove those lines but didn't for at least three years.
Absolutely, I'll add one, or add a check into an existing one.
@apeltzer @grst Added an additional profile for testing the samplesheet since the only one we had with adapters is test_full. Also, since I was already working on creating a short paired end profile for CI (https://github.com/nf-core/demultiplex/issues/189), I addressed both issues in this PR.
Suggesting to remove the adapter lines entirely from the samplesheet when
remove_adapters
is set to true. This should make bcl2fastq samplesheets compatible with bclconvert.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).