Closed BethYates closed 3 months ago
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nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit ac7b5ea
+| ✅ 131 tests passed |+
#| ❔ 21 tests were ignored |#
!| ❗ 1 tests had warnings |!
As discussed this morning:
- If you can find how to set
template_strings
=False
to only certain files, go for it :)- In the XML, add a placeholder for a variable that is not filled in by the pipeline to check that 1) the pipeline doesn't fail, and 2) the placeholder is not replaced.
I've added a placeholder " {{ TEST_NOT_REPLACED }}" in the xml template file and tested it works as expected. I wasn't able to get template_strings false working for individual files.
Genome note template is now passed as a parameter and can be either an XML or docx file. Examples of both templates are in the assets folder. The test config will output a genome note file based on the example XML file.
Added the latest XML
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).