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remove lane after tracking in id to ensure proper merging after mapping #1221

Merged
merged 15 commits into from
Sep 13, 2023
Merged

remove lane after tracking in id to ensure proper merging after mapping #1221

merged 15 commits into from
Sep 13, 2023

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FriederikeHanssen
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PR checklist

  • 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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Sep 11, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 65ae3d4

+| ✅ 140 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-09-12 19:07:41

@FriederikeHanssen
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tests are passign locally:

'Run UMI test' done.

tests/test_aligner_bwamem.yml .............................................................                                              [  6%]
tests/test_aligner_bwamem2.yml .............................................................                                             [ 13%]
tests/test_aligner_dragmap.yml ........................................................................                                  [ 22%]
tests/test_default.yml ......................................................                                                            [ 28%]
tests/test_fastp.yml ...................................................................................                                 [ 37%]
tests/test_freebayes.yml ............................................................................................................... [ 50%]
.........                                                                                                                                [ 51%]
tests/test_intervals.yml ............................................................................................................... [ 64%]
.....................                                                                                                                    [ 66%]
tests/test_save_mapped.yml .......................................................                                                       [ 73%]
tests/test_save_output_as_bam_only.yml ...................................................                                               [ 79%]
tests/test_skip_all_qc.yml .............................                                                                                 [ 82%]
tests/test_skip_markduplicates.yml ..................................................................................................... [ 93%]
...........                                                                                                                              [ 95%]
tests/test_umi.yml ..........................................                                                                            [100%] Keeping temporary directories and logs. Use '--kwd' or '--keep-workflow-wd' to disable this behaviour.


======================================================= 872 passed in 1593.92s (0:26:33) =======================================================

@FriederikeHanssen
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@nf-core-bot fix linting

@FriederikeHanssen
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Merging with failing tests as discussed. We'll investigate better tests for spark in a separate PR.

@FriederikeHanssen FriederikeHanssen merged commit 29a5c88 into nf-core:dev Sep 13, 2023
31 of 36 checks passed
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@maxulysse maxulysse maxulysse approved these changes

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@FriederikeHanssen @maxulysse @nf-core-bot