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Add and update - picard/gatk4 - addorreplacereadgroups #5302

Merged
merged 9 commits into from
Mar 20, 2024
Merged

Add and update - picard/gatk4 - addorreplacereadgroups #5302

merged 9 commits into from
Mar 20, 2024

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tomiles
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@tomiles tomiles commented Mar 20, 2024 •
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  • Update picard/addorreplacereadgroups with migrated tests to nf-test, and added support for cram input and output
  • Add the corresponding gatk4/addorreplacereadgroups

PR checklist

Closes #838

  • 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

@tomiles tomiles added the WIP Work in progress label Mar 20, 2024
@tomiles tomiles requested a review from matthdsm March 20, 2024 08:51
@matthdsm matthdsm enabled auto-merge March 20, 2024 12:31
@tomiles tomiles added Ready for Review and removed WIP Work in progress labels Mar 20, 2024
@matthdsm matthdsm added this pull request to the merge queue Mar 20, 2024
Merged via the queue into nf-core:master with commit c331b11 Mar 20, 2024
15 checks passed
jvfe added a commit to jvfe/modules that referenced this pull request Mar 20, 2024
@jvfe
Merge branch 'master' into nf-test_islandpath
f01d48c 
* master:
  Tcoffee tcs (nf-core#5288)
  Add and update - picard/gatk4 - addorreplacereadgroups (nf-core#5302)
  New module svtypersso (nf-core#5311)
@tomiles tomiles deleted the gatk-addorreplacereadgroups branch March 20, 2024 13:47
jvfe added a commit that referenced this pull request Mar 20, 2024
@jvfe
Merge branch 'master' into nf-test_phispy
a2bedc0 
* master:
  Add module nanofilt (#5290)
  Tcoffee tcs (#5288)
  Add and update - picard/gatk4 - addorreplacereadgroups (#5302)
  New module svtypersso (#5311)
tucano pushed a commit to tucano/modules that referenced this pull request Mar 20, 2024
@tomiles @matthdsm @tucano
Add and update - picard/gatk4 - addorreplacereadgroups (nf-core#5302)
e21479d 
* migrate picard_addorreplacereadgroups to nf-testand and add cram support

* remove unused code

* fix unstable checksums in tests

* remove crai and add meta 2 and 3

* update snap

* Duplicate as gatk4 module

* name conflict

---------

Co-authored-by: CMGG Cloud Team <[email protected]>
Co-authored-by: Matthias De Smet <[email protected]>
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
@tomiles @matthdsm @jennylsmith
Add and update - picard/gatk4 - addorreplacereadgroups (nf-core#5302)
25e4089 
* migrate picard_addorreplacereadgroups to nf-testand and add cram support

* remove unused code

* fix unstable checksums in tests

* remove crai and add meta 2 and 3

* update snap

* Duplicate as gatk4 module

* name conflict

---------

Co-authored-by: CMGG Cloud Team <[email protected]>
Co-authored-by: Matthias De Smet <[email protected]>
alexnater pushed a commit to alexnater/nf-core-modules that referenced this pull request Mar 21, 2024
@tomiles @matthdsm
Add and update - picard/gatk4 - addorreplacereadgroups (nf-core#5302)
deecc32 
* migrate picard_addorreplacereadgroups to nf-testand and add cram support

* remove unused code

* fix unstable checksums in tests

* remove crai and add meta 2 and 3

* update snap

* Duplicate as gatk4 module

* name conflict

---------

Co-authored-by: CMGG Cloud Team <[email protected]>
Co-authored-by: Matthias De Smet <[email protected]>
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@matthdsm matthdsm matthdsm approved these changes

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new module: gatk4/addorreplacereadgroups
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