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…cmsearch module has changed now
…ng subunit true in this pipelien
…hange multiqc test and snapshot
…nto add_gha_module_tests
mberacochea
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Oct 10, 2025
mberacochea
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Oct 10, 2025
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I'm chuffed that using the nf-core tools we can propagate bug-fixes/improvements across pipeline systematically :).
I left a couple of comments for the github action.. the one I would probably change is the nextflow edge one.
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| - name: Setup Nextflow latest-edge | ||
| uses: nf-core/setup-nextflow@v1 | ||
| with: | ||
| version: "latest-edge" |
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I wouldn't use the edge release.. it usually contains stuff that is not fully stable
| - name: Install nf-test | ||
| run: | | ||
| wget -qO- https://get.nf-test.com | bash | ||
| sudo mv nf-test /usr/local/bin/ |
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You can use this one instead:
- uses: nf-core/setup-nf-test@v1.3.6
with:
install-pdiff: true
which does the same internally... but it is maintained by nf-core, so hopefully bugs will get fixed
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makes sense!! I've changed it thank you :D
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Add github action that runs all nf-tests for all modules of the pipeline. Some details:
nf-core modules updatecommand for Update EXTRACTCOORDS module nf-modules#111 and Make extractcoords subunits splitting a parameter in rrna_extraction swf, also update more modules nf-modules#112