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add alignmentSieve #6693

Merged
merged 17 commits into from
Sep 27, 2024
Merged

add alignmentSieve #6693

merged 17 commits into from
Sep 27, 2024

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lpantano
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@lpantano lpantano commented Sep 25, 2024 •
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PR checklist

Add new sub-module to add feature in atacseq nf-core/atacseq#375

Closes #6690

  • 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.
  • Emit the versions.yml file.
  • 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

@lpantano
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@JoseEspinosa , I saw the issue you created and already started, there is at least one thing missing. The snapshot is not stable so the nf-test should test something else, and not the md5... Do you know alternatives?

@lpantano lpantano marked this pull request as ready for review September 25, 2024 15:21
@lpantano lpantano requested a review from a team as a code owner September 25, 2024 15:21
@lpantano lpantano requested review from vagkaratzas and removed request for a team September 25, 2024 15:21
@lpantano
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I think is ready, the errors there I believe is due to something else right not.

  remote: git: 'lariat' is not a git command. See 'git --help'.

JoseEspinosa
JoseEspinosa reviewed Sep 26, 2024
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Nice @lpantano! I just dropped some small suggestions.
Seems that the tests are not fixed yet though 😢

modules/nf-core/deeptools/alignmentsieve/meta.yml Outdated Show resolved Hide resolved
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JoseEspinosa
JoseEspinosa reviewed Sep 26, 2024
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Maybe try to delete the old snapshots and regenerate them and tests might work.

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agreed, there were some commits to use specific functions for BAM md5 but the snapshots are the old ones. I will update. Thanks!

lpantano and others added 5 commits September 26, 2024 12:59
@lpantano
update snapshot
bf7ec18
@lpantano @JoseEspinosa
fix keywords
9900781 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
@lpantano @JoseEspinosa
fix authors
ccf1fa5 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
@lpantano @JoseEspinosa
fix authors names
56791a8 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
@lpantano @JoseEspinosa
add to maintainers
c5ff229 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
@lpantano
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I think now it is good, but not sure why is waiting for status to be reported.

JoseEspinosa
JoseEspinosa approved these changes Sep 27, 2024
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LGTM!
I merged with master let's see if tests run now

@JoseEspinosa JoseEspinosa added this pull request to the merge queue Sep 27, 2024
Merged via the queue into nf-core:master with commit 5c2ab5d Sep 27, 2024
12 checks passed
herpov pushed a commit to herpov/modules that referenced this pull request Oct 2, 2024
@lpantano @apeltzer
@SPPearce @JoseEspinosa
add alignmentSieve (nf-core#6693)
56c7396 
* add alignmentSieve

* longer keywords

* add three keywords

* possible solution with size

* using logs instead of bam files

* fix meta

* Update modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test

Co-authored-by: Simon Pearce <[email protected]>

* update snapshot

* fix keywords

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

* fix authors

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

* fix authors names

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

* add to maintainers

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

---------

Co-authored-by: Alexander Peltzer <[email protected]>
Co-authored-by: Simon Pearce <[email protected]>
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
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@SPPearce SPPearce SPPearce left review comments

@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

@apeltzer apeltzer apeltzer approved these changes

@vagkaratzas vagkaratzas Awaiting requested review from vagkaratzas vagkaratzas was automatically assigned from nf-core/nf-test

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new module: DEEPTOOLS/ALIGNMENTSIEVE
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@lpantano @apeltzer @JoseEspinosa @SPPearce