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Add mobile element calling to raredisease #440

Merged
merged 27 commits into from
Jan 15, 2024
Merged

Add mobile element calling to raredisease #440

merged 27 commits into from
Jan 15, 2024

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peterpru
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@peterpru peterpru commented Nov 6, 2023 •
edited by jemten
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This PR aims to add a subworkflow on calling mobile element insertions using retroseq.

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).

@peterpru peterpru changed the title initial commit to log progress Add mobile element calling to raredisease Nov 6, 2023
@peterpru peterpru mentioned this pull request Nov 6, 2023
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github-actions bot commented Nov 6, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 967b7de

+| ✅ 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 08:59:39

@jemten jemten marked this pull request as ready for review January 9, 2024 15:55
@jemten jemten requested a review from ramprasadn January 10, 2024 12:09
ramprasadn
ramprasadn approved these changes Jan 15, 2024
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LGTM! 👍🏻

@ramprasadn ramprasadn merged commit 4158741 into nf-core:dev Jan 15, 2024
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@jemten jemten deleted the add-retroseq-to-pipeline branch January 15, 2024 12:12
@jemten jemten mentioned this pull request Jan 19, 2024
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@ramprasadn ramprasadn ramprasadn approved these changes

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@peterpru @jemten @ramprasadn