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Update glimpse/phase output channel to phased_variants #5172 #5174

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merged 20 commits into from
Mar 19, 2024

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@LouisLeNezet LouisLeNezet commented Mar 18, 2024

PR checklist

Rename phase_variant to phased_variants
Closes #5172

  • 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

@LouisLeNezet LouisLeNezet self-assigned this Mar 18, 2024
@LouisLeNezet LouisLeNezet requested a review from mashehu March 19, 2024 12:36
@LouisLeNezet LouisLeNezet enabled auto-merge March 19, 2024 13:58
@nf-core nf-core deleted a comment from mashehu Mar 19, 2024
@LouisLeNezet LouisLeNezet added this pull request to the merge queue Mar 19, 2024
Merged via the queue into nf-core:master with commit 7e56daa Mar 19, 2024
31 checks passed
@LouisLeNezet LouisLeNezet deleted the glimpse_phase branch March 19, 2024 15:17
jvfe added a commit to jvfe/modules that referenced this pull request Mar 19, 2024
* master:
  Fix test for FASTQ_FASTQC_UMITOOLS_FASTP which included an absolute path in the snapshot. (nf-core#5278)
  added new module lofraq/viterbi; solves new module: lofreq/viterbi nf-core#5158 (nf-core#5197)
  Update glimpse/phase output channel to phased_variants nf-core#5172 (nf-core#5174)
  Add module: GTFSORT (nf-core#5237)
  add nf-test to bedtools/sort - nf-core#3936 (nf-core#5221)
  addedd optional output channel for lib files (nf-core#5257)
vlebars pushed a commit to vlebars/modules that referenced this pull request Mar 20, 2024
…f-core#5174)

* Update glimpse/phase output channel to phased_variants

* Update nf-test

* Update tags and meta.yml

* Update tags in ligate

* Fix typo

* Delete non use argument

* Update tags in sbwf

* Update test data

* Update tag nftest

* Change extension individuals files

* Update genetic map

* Change map by chromosome

* Update vcf_impute_glimpse nftest

* Update to phased_variants

* Update glimpse concordance

* Update modules/nf-core/glimpse/ligate/meta.yml

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

---------

Co-authored-by: Matthias Hörtenhuber <[email protected]>
tucano pushed a commit to tucano/modules that referenced this pull request Mar 20, 2024
…f-core#5174)

* Update glimpse/phase output channel to phased_variants

* Update nf-test

* Update tags and meta.yml

* Update tags in ligate

* Fix typo

* Delete non use argument

* Update tags in sbwf

* Update test data

* Update tag nftest

* Change extension individuals files

* Update genetic map

* Change map by chromosome

* Update vcf_impute_glimpse nftest

* Update to phased_variants

* Update glimpse concordance

* Update modules/nf-core/glimpse/ligate/meta.yml

Co-authored-by: Matthias Hörtenhuber <[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
…f-core#5174)

* Update glimpse/phase output channel to phased_variants

* Update nf-test

* Update tags and meta.yml

* Update tags in ligate

* Fix typo

* Delete non use argument

* Update tags in sbwf

* Update test data

* Update tag nftest

* Change extension individuals files

* Update genetic map

* Change map by chromosome

* Update vcf_impute_glimpse nftest

* Update to phased_variants

* Update glimpse concordance

* Update modules/nf-core/glimpse/ligate/meta.yml

Co-authored-by: Matthias Hörtenhuber <[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
…f-core#5174)

* Update glimpse/phase output channel to phased_variants

* Update nf-test

* Update tags and meta.yml

* Update tags in ligate

* Fix typo

* Delete non use argument

* Update tags in sbwf

* Update test data

* Update tag nftest

* Change extension individuals files

* Update genetic map

* Change map by chromosome

* Update vcf_impute_glimpse nftest

* Update to phased_variants

* Update glimpse concordance

* Update modules/nf-core/glimpse/ligate/meta.yml

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

---------

Co-authored-by: Matthias Hörtenhuber <[email protected]>
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Glimpse tools output channel name inconsistent
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