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Fix KmerFinder DB and relative paths resolution issues #231

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Daniel-VM merged 11 commits into from
Jul 18, 2025
Merged

Fix KmerFinder DB and relative paths resolution issues #231

Daniel-VM merged 11 commits into from
Jul 18, 2025

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@Daniel-VM Daniel-VM commented Apr 9, 2025 •
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PR checklist

  • 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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/bacass branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

PR Description

This PR addresses path-related issues when processing the input samplesheet:

  • Fixed incorrect KmerFinder database paths
  • Resolved errors with symbolic links and local paths

Close #215
Close #188

Daniel-VM added a commit to Daniel-VM/bacass that referenced this pull request Apr 9, 2025
@Daniel-VM
update changelog in nf-core#231
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Daniel-VM added a commit to Daniel-VM/bacass that referenced this pull request Jun 24, 2025
@Daniel-VM
update changelog in nf-core#231
6b59c3f
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nf-core-bot commented Jun 24, 2025 •
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@Daniel-VM Daniel-VM marked this pull request as ready for review June 24, 2025 10:30
@Daniel-VM Daniel-VM mentioned this pull request Jun 26, 2025
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Daniel-VM added a commit to Daniel-VM/bacass that referenced this pull request Jul 7, 2025
@Daniel-VM
update changelog in nf-core#231
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d4straub
d4straub reviewed Jul 7, 2025
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You would not expect changes in the files that are listed in https://github.com/nf-core/bacass/actions/runs/16113916911/job/45463464679?pr=231, would you? I am asking because maybe the content of a few unstable files is still checked in that test.

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Daniel-VM commented Jul 7, 2025

You would not expect changes in the files that are listed in https://github.com/nf-core/bacass/actions/runs/16113916911/job/45463464679?pr=231, would you? I am asking because maybe the content of a few unstable files is still checked in that test.

No. As far as I can see , there are files that don't match test snapshot, however, I haven't modify them in this PR.

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d4straub commented Jul 7, 2025 •
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No. As far as I can see , there are files that don't match test snapshot, however, I haven't modify them in this PR.

Thanks. I'll add some more test profiles and investigate a bit more what can be done to get more stable outcomes.

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Daniel-VM commented Jul 7, 2025

Thanks for the update. I’m not entirely sure what’s causing these discrepancies... The #246 passed without any errors, and I did not modify any related files. If you’d need help to dig into the snapshots just let me know 👍🏾

Daniel-VM added a commit to Daniel-VM/bacass that referenced this pull request Jul 9, 2025
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update changelog in nf-core#231
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d4straub commented Jul 9, 2025

Failing checks for shards 3, 4, and 7 appears to be that "CAT_FASTQ" isnt executed for test profiles test_hybrid & test_hybrid_dragonflye & test_liftoff.
This doesnt seem intended, is it? I am just still skeptic with the checks. Please ping me in case you have any unexpected trouble with those.

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Daniel-VM commented Jul 14, 2025

Failing checks for shards 3, 4, and 7 appears to be that "CAT_FASTQ" isnt executed for test profiles test_hybrid & test_hybrid_dragonflye & test_liftoff. This doesnt seem intended, is it? I am just still skeptic with the checks. Please ping me in case you have any unexpected trouble with those.

@d4straub , fixed tests that failed in relation to the CAT_FASTQ module

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Changes look all good to me, but I dont get why that CAT_FASTQ* processes are now executed but were before not. Just to make sure, they are supposed to be executed in those tests?

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Daniel-VM commented Jul 15, 2025 •
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Changes look all good to me, but I dont get why that CAT_FASTQ* processes are not executed but were before not. Just to make sure, they are supposed to be executed in those tests?

CAT_FASTQ* should be executed when samples are resequenced (repeated sample entries in the input). For instance: https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_short_reseq.tsv

However, I have noticed that CAT_FASTQ* is getting executed even when samples are not resequenced. This is not the expected behavior. Fix in comming.

(Actually, it was correctly working here: #248).

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Daniel-VM commented Jul 15, 2025

@nf-core-bot fix linting

@Daniel-VM Daniel-VM requested a review from d4straub July 17, 2025 07:18
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Changes look fine to me.
It looks to me as if the db name change of kmerfinderdb was fixed, I am confused though how relative paths were fixed, i dont see anywhere the file() expression added that was argued before is necessary.

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Daniel-VM commented Jul 17, 2025

@nf-core-bot fix linting

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Daniel-VM commented Jul 17, 2025

Changes look fine to me. It looks to me as if the db name change of kmerfinderdb was fixed, I am confused though how relative paths were fixed, i dont see anywhere the file() expression added that was argued before is necessary.

You are completely right... the handling of symblinks were not properly setup for input samples 😞 (I thought it was fixed but no).

I have added here a function to manage symbolic links for input samples.

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d4straub approved these changes Jul 18, 2025
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LGTM!

@Daniel-VM Daniel-VM merged commit f5e4786 into nf-core:dev Jul 18, 2025
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