Closed jmuhlich closed 4 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 68251e9
+| ✅ 165 tests passed |+
#| ❔ 1 tests were ignored |#
!| ❗ 25 tests had warnings |!
Thank you @jmuhlich for linking the most recent changes :) it looks good to me 👍 Thanks to @maxulysse for finding those sneaky issues, I would rather wait for jeremy to take a look
PR checklist
nf-core lint
).nf-test test main.nf.test -profile test,docker
).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).~This adds support for two different styles of input sample sheet: one row per cycle per sample (
input_cycle
) and one row per sample (input_sample
). Validation of much of the sample sheets and marker sheet file is done in python scripts, but work is already ongoing to port this logic directly into Groovy/Nextflow.An nf-test test suite for the pipeline and key workflows has also been added. Note that the Nextflow code does some "naughty" things around re-parsing the input sample sheet rather than only consuming the already parsed values from the proper input channel, so the nf-test setup code has a lot of redundancies. As part of porting the python validation code into Groovy we will address this issue and make the workflows more "functional" and clean up the test definitions.