Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Merged
merged 20 commits into from
Mar 19, 2024
Merged

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

merged 20 commits into from
Mar 19, 2024

Conversation

LouisLeNezet
Copy link
Contributor

@LouisLeNezet LouisLeNezet commented Mar 18, 2024 •
edited
Loading

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
@jvfe
Merge branch 'master' into nf-test_phispy
e16f6f9 
* 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
@LouisLeNezet @mashehu
Update glimpse/phase output channel to phased_variants nf-core#5172 (n…
a27d67c 
…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
@LouisLeNezet @mashehu @tucano
Update glimpse/phase output channel to phased_variants nf-core#5172 (n…
9fe0eee 
…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
@LouisLeNezet @mashehu @jennylsmith
Update glimpse/phase output channel to phased_variants nf-core#5172 (n…
e8daf7c 
…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
@LouisLeNezet @mashehu
Update glimpse/phase output channel to phased_variants nf-core#5172 (n…
74b4561 
…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]>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@mashehu mashehu Awaiting requested review from mashehu

Assignees

@LouisLeNezet LouisLeNezet

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Glimpse tools output channel name inconsistent
2 participants
@LouisLeNezet @FriederikeHanssen