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convert bam to cram #340

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Merged
merged 2 commits into from
May 5, 2023
Merged

convert bam to cram #340

merged 2 commits into from
May 5, 2023

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@ramprasadn
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@ramprasadn ramprasadn commented May 5, 2023 •
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PR checklist

This feature adds the option to generate and publish cram files instead of bams.

  • 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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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).

@ramprasadn ramprasadn linked an issue May 5, 2023 that may be closed by this pull request
Compress bam to cram #327
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github-actions bot commented May 5, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 12217db

+| ✅ 154 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.0.0'
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-05 13:25:57

@ramprasadn ramprasadn requested a review from jemten May 5, 2023 13:32
@ramprasadn ramprasadn marked this pull request as ready for review May 5, 2023 13:32
jemten
jemten approved these changes May 5, 2023
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Nice and clean implementation :)

@ramprasadn ramprasadn merged commit 12395f2 into nf-core:devplaceholder May 5, 2023
@ramprasadn ramprasadn deleted the bamtocram branch May 5, 2023 16:36
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@jemten jemten jemten approved these changes

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Compress bam to cram

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@ramprasadn @jemten