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Remove unnecessary .view() in subworkflows/nf-core/vcf_phase_shapeit5 & tests/modules/nf-core/shapeit5/ligate/main.nf #5280

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merged 6 commits into from Mar 20, 2024
Merged

Remove unnecessary .view() in subworkflows/nf-core/vcf_phase_shapeit5 & tests/modules/nf-core/shapeit5/ligate/main.nf #5280

merged 6 commits into from Mar 20, 2024

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dimple-aspiring-cat
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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

@dimple-aspiring-cat dimple-aspiring-cat self-assigned this Mar 19, 2024
@LouisLeNezet
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Link to #5231

@LouisLeNezet LouisLeNezet added this pull request to the merge queue Mar 20, 2024
@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to failed status checks Mar 20, 2024
@LouisLeNezet LouisLeNezet added this pull request to the merge queue Mar 20, 2024
Merged via the queue into nf-core:master with commit dcf17cc Mar 20, 2024
15 checks passed
vlebars pushed a commit to vlebars/modules that referenced this pull request Mar 20, 2024
@dimple-aspiring-cat @LouisLeNezet
Remove unnecessary .view() in subworkflows/nf-core/vcf_phase_shapeit5…
bd1ff1f 
… & tests/modules/nf-core/shapeit5/ligate/main.nf (nf-core#5280)

* .view() deleted

* Delete unecessary view

* Update licence

* Bcftools view compressed output

* Update licence

---------

Co-authored-by: Dimple Adiwal <dadiwal@genossh.genouest.org>
Co-authored-by: Dimple Adiwal <dadiwal@cl1n020.genouest.org>
Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@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
@dimple-aspiring-cat @LouisLeNezet @tucano
Remove unnecessary .view() in subworkflows/nf-core/vcf_phase_shapeit5…
cfac3f2 
… & tests/modules/nf-core/shapeit5/ligate/main.nf (nf-core#5280)

* .view() deleted

* Delete unecessary view

* Update licence

* Bcftools view compressed output

* Update licence

---------

Co-authored-by: Dimple Adiwal <dadiwal@genossh.genouest.org>
Co-authored-by: Dimple Adiwal <dadiwal@cl1n020.genouest.org>
Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
@dimple-aspiring-cat @LouisLeNezet @jennylsmith
Remove unnecessary .view() in subworkflows/nf-core/vcf_phase_shapeit5…
fba9a17 
… & tests/modules/nf-core/shapeit5/ligate/main.nf (nf-core#5280)

* .view() deleted

* Delete unecessary view

* Update licence

* Bcftools view compressed output

* Update licence

---------

Co-authored-by: Dimple Adiwal <dadiwal@genossh.genouest.org>
Co-authored-by: Dimple Adiwal <dadiwal@cl1n020.genouest.org>
Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>
alexnater pushed a commit to alexnater/nf-core-modules that referenced this pull request Mar 21, 2024
@dimple-aspiring-cat @LouisLeNezet
Remove unnecessary .view() in subworkflows/nf-core/vcf_phase_shapeit5…
52e3c28 
… & tests/modules/nf-core/shapeit5/ligate/main.nf (nf-core#5280)

* .view() deleted

* Delete unecessary view

* Update licence

* Bcftools view compressed output

* Update licence

---------

Co-authored-by: Dimple Adiwal <dadiwal@genossh.genouest.org>
Co-authored-by: Dimple Adiwal <dadiwal@cl1n020.genouest.org>
Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>
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@LouisLeNezet LouisLeNezet LouisLeNezet approved these changes

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