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Fix for getting chr sizes when fai is given #479

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Merged
merged 2 commits into from
Jan 15, 2024
Merged

Fix for getting chr sizes when fai is given #479

merged 2 commits into from
Jan 15, 2024

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@jemten
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@jemten jemten commented Jan 12, 2024 •
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Fix that tells the local module GET_CHROM_SIZES to use supplied fai file when given by the user.

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/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).

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github-actions bot commented Jan 12, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 615039f

+| ✅ 155 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.

❔ 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
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-15 08:15:07

@jemten jemten marked this pull request as ready for review January 12, 2024 16:47
@jemten jemten requested a review from ramprasadn January 12, 2024 16:47
ramprasadn
ramprasadn approved these changes Jan 15, 2024
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🚀

@jemten jemten merged commit 2dbd6ea into nf-core:dev Jan 15, 2024
@jemten jemten deleted the fixing_order branch January 15, 2024 08:24
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@ramprasadn ramprasadn ramprasadn approved these changes

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@jemten @ramprasadn