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4557 new module kaijumergeoutputs + stub Kraken2/Kraken2 #5249

Merged
merged 11 commits into from
Mar 20, 2024
Merged

4557 new module kaijumergeoutputs + stub Kraken2/Kraken2 #5249

merged 11 commits into from
Mar 20, 2024

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Joon-Klaps
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PR checklist

Closes #4557

  • 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

@Joon-Klaps Joon-Klaps requested a review from nvnieuwk March 19, 2024 13:18
@Joon-Klaps Joon-Klaps requested review from a team, JoseEspinosa and drpatelh as code owners March 19, 2024 13:18
nvnieuwk
nvnieuwk reviewed Mar 19, 2024
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@Joon-Klaps Joon-Klaps requested a review from nvnieuwk March 19, 2024 15:44
nvnieuwk
nvnieuwk approved these changes Mar 20, 2024
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@nvnieuwk nvnieuwk left a comment

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LGTM!

@Joon-Klaps Joon-Klaps added this pull request to the merge queue Mar 20, 2024
Merged via the queue into nf-core:master with commit 653218e Mar 20, 2024
19 checks passed
@Joon-Klaps Joon-Klaps deleted the 4557-new-module-kaijumergeoutputs branch March 20, 2024 09:06
vlebars pushed a commit to vlebars/modules that referenced this pull request Mar 20, 2024
@Joon-Klaps
4557 new module kaijumergeoutputs + stub Kraken2/Kraken2 (nf-core#5249)
dff49f8 
* init kaiju-mergedOutputs

* init kaiju_mergeoutputs

* Update file paths and add test case for stub in kraken2_kraken2

* adressing comments reviewer

* Fix variable assignment in db.config and nodb.config

* Add docker.fixOwnership to process block in db.config and nodb.config

* Update process configuration to fix ownership issue

* typo

* Remove docker.fixOwnership from db.config
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
@Joon-Klaps @tucano
4557 new module kaijumergeoutputs + stub Kraken2/Kraken2 (nf-core#5249)
66be4a7 
* init kaiju-mergedOutputs

* init kaiju_mergeoutputs

* Update file paths and add test case for stub in kraken2_kraken2

* adressing comments reviewer

* Fix variable assignment in db.config and nodb.config

* Add docker.fixOwnership to process block in db.config and nodb.config

* Update process configuration to fix ownership issue

* typo

* Remove docker.fixOwnership from db.config
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
@Joon-Klaps @jennylsmith
4557 new module kaijumergeoutputs + stub Kraken2/Kraken2 (nf-core#5249)
b98e417 
* init kaiju-mergedOutputs

* init kaiju_mergeoutputs

* Update file paths and add test case for stub in kraken2_kraken2

* adressing comments reviewer

* Fix variable assignment in db.config and nodb.config

* Add docker.fixOwnership to process block in db.config and nodb.config

* Update process configuration to fix ownership issue

* typo

* Remove docker.fixOwnership from db.config
alexnater pushed a commit to alexnater/nf-core-modules that referenced this pull request Mar 21, 2024
@Joon-Klaps
4557 new module kaijumergeoutputs + stub Kraken2/Kraken2 (nf-core#5249)
5cb5da7 
* init kaiju-mergedOutputs

* init kaiju_mergeoutputs

* Update file paths and add test case for stub in kraken2_kraken2

* adressing comments reviewer

* Fix variable assignment in db.config and nodb.config

* Add docker.fixOwnership to process block in db.config and nodb.config

* Update process configuration to fix ownership issue

* typo

* Remove docker.fixOwnership from db.config
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Reviewers

@nvnieuwk nvnieuwk nvnieuwk approved these changes

@JoseEspinosa JoseEspinosa Awaiting requested review from JoseEspinosa

@drpatelh drpatelh Awaiting requested review from drpatelh

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new module: kaiju/mergeOutputs
2 participants
@Joon-Klaps @nvnieuwk