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Few fixes #570

Merged
merged 19 commits into from
Jun 24, 2024
Merged

Few fixes #570

merged 19 commits into from
Jun 24, 2024

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ramprasadn
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@ramprasadn ramprasadn commented Jun 20, 2024 •
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PR checklist

Added

  • Two new parameters mbuffer_mem and samtools_sort_threads to control resources given to mbuffer and samtools sort in the bwameme module #570

Changed

  • readcount_intervals parameter is now mandatory for running germlinecnvcaller. #570

Fixed

  • Docker manifest error from gnu-wget container #570

  • 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>).

  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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 Jun 20, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ca4cdad

+| ✅ 185 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • 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/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • 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
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-24 08:41:13

@ramprasadn ramprasadn marked this pull request as ready for review June 21, 2024 06:45
jemten
jemten reviewed Jun 24, 2024
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Looks good. Would be good to clarify the readcount_intervals file.

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@ramprasadn ramprasadn requested a review from jemten June 24, 2024 08:28
jemten
jemten approved these changes Jun 24, 2024
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👍

@ramprasadn ramprasadn merged commit 744b841 into dev Jun 24, 2024
6 checks passed
@jemten jemten deleted the patch branch June 24, 2024 09:03
@ramprasadn ramprasadn mentioned this pull request Jun 25, 2024
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@jemten jemten jemten approved these changes

@rannick rannick Awaiting requested review from rannick

@Lucpen Lucpen Awaiting requested review from Lucpen

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@ramprasadn @jemten