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added pcne module#11307

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riccabolla wants to merge 28 commits intonf-core:masterfrom
riccabolla:new-module-pcne
Draft

added pcne module#11307
riccabolla wants to merge 28 commits intonf-core:masterfrom
riccabolla:new-module-pcne

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@riccabolla riccabolla commented Apr 25, 2026

PR checklist

Closes #XXX

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@riccabolla riccabolla marked this pull request as draft April 25, 2026 15:31
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famosab commented Apr 27, 2026

Please join the nf-core organization on GitHub to enable the CI-tests to run on your PR. You can request to join the organization via #github-invitations in the nf-core slack. You can join the nf-core slack via https://nf-co.re/join.

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riccabolla commented Apr 27, 2026

Please join the nf-core organization on GitHub to enable the CI-tests to run on your PR. You can request to join the organization via #github-invitations in the nf-core slack. You can join the nf-core slack via https://nf-co.re/join.

Thank you! Done!

@riccabolla riccabolla self-assigned this Apr 27, 2026
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famosab commented Apr 27, 2026

@nf-core-bot fix linting

famosab
famosab reviewed Apr 27, 2026
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Thank you for your contribution to nf-core! We really appreciate it. I added a few comments to your PR.

Comment thread modules/nf-core/pcne/tests/main.nf.test Outdated
Comment thread modules/nf-core/pcne/tests/main.nf.test Outdated
Comment thread modules/nf-core/pcne/main.nf Outdated
Comment thread modules/nf-core/pcne/main.nf
Comment thread modules/nf-core/pcne/main.nf
Comment thread modules/nf-core/pcne/meta.yml
famosab
famosab reviewed Apr 27, 2026
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Comment thread modules/nf-core/pcne/main.nf Outdated
riccabolla and others added 15 commits April 28, 2026 13:49
@riccabolla @famosab
Update modules/nf-core/pcne/main.nf
ba6285f 
Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
@riccabolla
Refactor test assertions to use sanitized output
749835e
@riccabolla
Merge branch 'nf-core:master' into new-module-pcne
6efac0c
@riccabolla
added test snap
b7bbd1d
@riccabolla
Update pcne version from 3.3.0 to 3.3.1
8db1f55
@riccabolla
Update PCNE container version to 3.3.1
c1825c1
@riccabolla
fixed meta.yml
c86f5e7
@riccabolla
Refactor input structure in meta.yml for clarity
1ec3b0e
@riccabolla
Refactor PCNE process for improved readability
30452f8
@riccabolla
Update PCNE version from 3.3.0 to 3.3.1
4c8aaa7
@riccabolla
Merge branch 'nf-core:master' into new-module-pcne
e59abf0
@riccabolla
Update test inputs to use module test data paths
f505ea0
@riccabolla
whitespace fixing
cd1f842 
Corrected indentation for description field in meta.yml.
@riccabolla
Fix input array formatting in main.nf.test
9728f9a
@riccabolla
Merge branch 'master' into new-module-pcne
1c699eb
famosab
famosab reviewed Apr 29, 2026
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Comment thread modules/nf-core/pcne/tests/main.nf.test Outdated

then {
assert process.success
assert snapshot(sanitizeOutput(process.out)).match()
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I think it makes sense to only assert the name of the log file? The log file probably has some timestamp that then changes the md5sum :)

famosab
famosab reviewed Apr 29, 2026
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Comment thread modules/nf-core/pcne/tests/main.nf.test.snap Outdated
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