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gatk4_asereadcounter add updated meta and nf-tests #5164

Merged
merged 9 commits into from
Mar 20, 2024
Merged

gatk4_asereadcounter add updated meta and nf-tests #5164

merged 9 commits into from
Mar 20, 2024

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Lucpen
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@Lucpen Lucpen commented Mar 18, 2024

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.
  • 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

@Lucpen Lucpen changed the title feat updated meta gatk4_asereadcounter add updated meta Mar 19, 2024
@Lucpen Lucpen marked this pull request as ready for review March 19, 2024 09:23
mashehu
mashehu requested changes Mar 19, 2024
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modules/nf-core/gatk4/asereadcounter/meta.yml Outdated Show resolved Hide resolved
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modules/nf-core/gatk4/asereadcounter/tests/nextflow.config Outdated
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You can remove this file.

If the old pytests files are still there (including the entry in the tags.yml) please remove them as well

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Done!

@Lucpen Lucpen requested a review from a team as a code owner March 19, 2024 11:44
@Lucpen Lucpen requested review from koenbossers and removed request for a team March 19, 2024 11:44
@Lucpen Lucpen changed the title gatk4_asereadcounter add updated meta gatk4_asereadcounter add updated meta and nf-tests Mar 19, 2024
mashehu
mashehu approved these changes Mar 20, 2024
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Sorry, lost track of this one in the hackathon hubbub. looking good now!

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Lucpen commented Mar 20, 2024

Np, thanks!

@Lucpen Lucpen added this pull request to the merge queue Mar 20, 2024
Merged via the queue into master with commit 89cf292 Mar 20, 2024
9 checks passed
@mashehu mashehu deleted the asereadcounter_add_meta branch March 20, 2024 09:09
vlebars pushed a commit to vlebars/modules that referenced this pull request Mar 20, 2024
@Lucpen @mashehu
gatk4_asereadcounter add updated meta and nf-tests (nf-core#5164)
42a834c 
* feat updated meta

* feat add nf-tests

* Update modules/nf-core/gatk4/asereadcounter/meta.yml

Co-authored-by: Matthias Hörtenhuber <[email protected]>

* Update modules/nf-core/gatk4/asereadcounter/meta.yml

Co-authored-by: Matthias Hörtenhuber <[email protected]>

* applyed reviewers suggestions

* modified pytest_modules.yml

---------

Co-authored-by: [email protected] <[email protected]>
Co-authored-by: Matthias Hörtenhuber <[email protected]>
jvfe added a commit to jvfe/modules that referenced this pull request Mar 20, 2024
@jvfe
Merge branch 'master' into nf-test_islandpath
2be1844 
* master:
  Added contrast limited adaptive histogram equalization module (nf-core#5268)
  Leviosam2 index (nf-core#5316)
  Add subworkflow mapAD (nf-core#5239)
  Remove AMRFinderPlus DB update on each invocation (nf-core#5232)
  Revert "add paths in output directive in cellranger cout module" (nf-core#5306)
  Revert "update kallistobustools count output list" (nf-core#5307)
  Igv reports (nf-core#5263)
  Remove unnecessary .view() in subworkflows/nf-core/vcf_phase_shapeit5 & tests/modules/nf-core/shapeit5/ligate/main.nf (nf-core#5280)
  Add wittyer as module (nf-core#5171)
  Bamstats (nf-core#4474)
  gatk4_asereadcounter add updated meta and nf-tests (nf-core#5164)
  4557 new module kaijumergeoutputs + stub Kraken2/Kraken2 (nf-core#5249)
  add cram/index support to bwamem2 (nf-core#5248)
  Add README to modules build with Docker (nf-core#4935)
  update paths for VEP (nf-core#5281)
  nf-test bases2fastq (nf-core#5272)
  Add module seqfu/stats (nf-core#5275)
jvfe added a commit to jvfe/modules that referenced this pull request Mar 20, 2024
@jvfe
Merge branch 'master' into nf-test_phispy
294a9c0 
* master:
  Added contrast limited adaptive histogram equalization module (nf-core#5268)
  Leviosam2 index (nf-core#5316)
  Add subworkflow mapAD (nf-core#5239)
  Remove AMRFinderPlus DB update on each invocation (nf-core#5232)
  Revert "add paths in output directive in cellranger cout module" (nf-core#5306)
  Revert "update kallistobustools count output list" (nf-core#5307)
  Igv reports (nf-core#5263)
  Remove unnecessary .view() in subworkflows/nf-core/vcf_phase_shapeit5 & tests/modules/nf-core/shapeit5/ligate/main.nf (nf-core#5280)
  Add wittyer as module (nf-core#5171)
  Bamstats (nf-core#4474)
  gatk4_asereadcounter add updated meta and nf-tests (nf-core#5164)
  4557 new module kaijumergeoutputs + stub Kraken2/Kraken2 (nf-core#5249)
  add cram/index support to bwamem2 (nf-core#5248)
  Add README to modules build with Docker (nf-core#4935)
  update paths for VEP (nf-core#5281)
  nf-test bases2fastq (nf-core#5272)
  Add module seqfu/stats (nf-core#5275)
  Added gt/gff3validator (nf-core#4718)
  Added liftoff (nf-core#5209)
tucano pushed a commit to tucano/modules that referenced this pull request Mar 20, 2024
@Lucpen @mashehu @tucano
gatk4_asereadcounter add updated meta and nf-tests (nf-core#5164)
2074673 
* feat updated meta

* feat add nf-tests

* Update modules/nf-core/gatk4/asereadcounter/meta.yml

Co-authored-by: Matthias Hörtenhuber <[email protected]>

* Update modules/nf-core/gatk4/asereadcounter/meta.yml

Co-authored-by: Matthias Hörtenhuber <[email protected]>

* applyed reviewers suggestions

* modified pytest_modules.yml

---------

Co-authored-by: [email protected] <[email protected]>
Co-authored-by: Matthias Hörtenhuber <[email protected]>
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
@Lucpen @mashehu @jennylsmith
gatk4_asereadcounter add updated meta and nf-tests (nf-core#5164)
15563ee 
* feat updated meta

* feat add nf-tests

* Update modules/nf-core/gatk4/asereadcounter/meta.yml

Co-authored-by: Matthias Hörtenhuber <[email protected]>

* Update modules/nf-core/gatk4/asereadcounter/meta.yml

Co-authored-by: Matthias Hörtenhuber <[email protected]>

* applyed reviewers suggestions

* modified pytest_modules.yml

---------

Co-authored-by: [email protected] <[email protected]>
Co-authored-by: Matthias Hörtenhuber <[email protected]>
alexnater pushed a commit to alexnater/nf-core-modules that referenced this pull request Mar 21, 2024
@Lucpen @mashehu
gatk4_asereadcounter add updated meta and nf-tests (nf-core#5164)
ee83242 
* feat updated meta

* feat add nf-tests

* Update modules/nf-core/gatk4/asereadcounter/meta.yml

Co-authored-by: Matthias Hörtenhuber <[email protected]>

* Update modules/nf-core/gatk4/asereadcounter/meta.yml

Co-authored-by: Matthias Hörtenhuber <[email protected]>

* applyed reviewers suggestions

* modified pytest_modules.yml

---------

Co-authored-by: [email protected] <[email protected]>
Co-authored-by: Matthias Hörtenhuber <[email protected]>
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@mashehu mashehu mashehu approved these changes

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