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Add module: GTFSORT #5237

Merged
merged 4 commits into from
Mar 19, 2024
Merged

Add module: GTFSORT #5237

merged 4 commits into from
Mar 19, 2024

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georgiakes
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PR checklist

Closes #4262

  • Module for gtfsort.
  • 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 GTFSORT --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda

@georgiakes georgiakes requested a review from a team as a code owner March 19, 2024 12:07
@georgiakes georgiakes requested review from CarsonJM and removed request for a team March 19, 2024 12:07
itrujnara
itrujnara reviewed Mar 19, 2024
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@itrujnara itrujnara left a comment

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My only major concern is the meta map, which I foresee being useful inside pipelines. See code comments for details. Other than that, only minor formatting issues.

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itrujnara
itrujnara approved these changes Mar 19, 2024
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Free to merge once formatting is addressed

@georgiakes georgiakes added this pull request to the merge queue Mar 19, 2024
Merged via the queue into nf-core:master with commit 9b14b5f Mar 19, 2024
11 checks passed
@georgiakes georgiakes deleted the gtfsort branch March 19, 2024 15:06
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
@georgiakes
Add module: GTFSORT (nf-core#5237)
e2d7d36 
* Initial commit

* Fix formatting
tucano pushed a commit to tucano/modules that referenced this pull request Mar 20, 2024
@georgiakes @tucano
Add module: GTFSORT (nf-core#5237)
7f7a3ae 
* Initial commit

* Fix formatting
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
@georgiakes @jennylsmith
Add module: GTFSORT (nf-core#5237)
632ef50 
* Initial commit

* Fix formatting
alexnater pushed a commit to alexnater/nf-core-modules that referenced this pull request Mar 21, 2024
@georgiakes
Add module: GTFSORT (nf-core#5237)
f3b51f7 
* Initial commit

* Fix formatting
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@itrujnara itrujnara itrujnara approved these changes

@CarsonJM CarsonJM Awaiting requested review from CarsonJM CarsonJM was automatically assigned from nf-core/nf-test

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new module: gtfsort
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@georgiakes @itrujnara