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nf-test bases2fastq #5272

Merged
merged 5 commits into from Mar 20, 2024
Merged

nf-test bases2fastq #5272

merged 5 commits into from Mar 20, 2024

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kobelavaerts
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PR checklist

Closes #5222

  • 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

@kobelavaerts kobelavaerts requested review from edmundmiller and a team as code owners March 19, 2024 15:36
@Joon-Klaps
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@nf-core-bot fix linting

edmundmiller
edmundmiller approved these changes Mar 19, 2024
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@edmundmiller edmundmiller left a comment

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LGTM!

@edmundmiller edmundmiller added this pull request to the merge queue Mar 20, 2024
Merged via the queue into nf-core:master with commit c2342b4 Mar 20, 2024
9 checks passed
vlebars pushed a commit to vlebars/modules that referenced this pull request Mar 20, 2024
@kobelavaerts @nf-core-bot @Joon-Klaps
nf-test bases2fastq (nf-core#5272)
657ccd9 
* add nf-test to bases2fastq

* add untar tag to tags.yml

* added stub

* [automated] Fix linting with Prettier

---------

Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>
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
@kobelavaerts @nf-core-bot
@Joon-Klaps @tucano
nf-test bases2fastq (nf-core#5272)
dce2a09 
* add nf-test to bases2fastq

* add untar tag to tags.yml

* added stub

* [automated] Fix linting with Prettier

---------

Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
@kobelavaerts @nf-core-bot
@Joon-Klaps @jennylsmith
nf-test bases2fastq (nf-core#5272)
ef4cfcc 
* add nf-test to bases2fastq

* add untar tag to tags.yml

* added stub

* [automated] Fix linting with Prettier

---------

Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>
alexnater pushed a commit to alexnater/nf-core-modules that referenced this pull request Mar 21, 2024
@kobelavaerts @nf-core-bot @Joon-Klaps
nf-test bases2fastq (nf-core#5272)
37a2570 
* add nf-test to bases2fastq

* add untar tag to tags.yml

* added stub

* [automated] Fix linting with Prettier

---------

Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>
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@edmundmiller edmundmiller edmundmiller approved these changes

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add nf-test to bases2fastq
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@kobelavaerts @Joon-Klaps @edmundmiller @nf-core-bot