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Patch Release 2.4.3 #865

Merged
merged 19 commits into from
Mar 24, 2022
Merged

Patch Release 2.4.3 #865

merged 19 commits into from
Mar 24, 2022

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jfy133
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@jfy133 jfy133 commented Mar 24, 2022

Patch release 2.4.3

Fixed

  • #828 Improved error message if required metagenomic screening parameters not set correctly
  • #836 Remove deprecated parameters from test profiles
  • #838 Fix --snpcapture_bed files not being picked up by Nextflow (❤ to @meganemichel for reporting)
  • #843 Re-add direct piping of AdapterRemovalFixPrefix to pigz
  • #844 Fixed reference masking prior to pmdtools
  • #845 Updates parameter documention to specify -s preseq parameter also applies to lc_extrap
  • #851 Fixes a file-name clash during additional_library_merge, post-BAM trimming of different UDG treated libraries of a sample
  • Renamed a range of MultiQC general stats table headers to improve clarity, documentation has been updated accordingly
  • #857 Corrected samtools fastq flag to retain read-pair information when converting off-target BAM files to fastq in paired-end mapping (❤ to @alexhbnr for reporting)
  • #858 Corrected tutorials to reflect updated BAM trimming flags (❤ to @marcel-keller for reporting)

Dependencies

  • #829 Bumped sequencetools: 1.4.0.5 -> 1.5.2
  • Bumped MultiQC: 1.11 -> 1.12 (for run-time optimisation and tool citation information)

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
    • If necessary, also make a PR on the nf-core/eager 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).
  • 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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Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

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  • Fix the markdown errors
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Thanks again for your contribution!

@jfy133 jfy133 requested a review from a team March 24, 2022 07:43
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@maxulysse maxulysse left a comment

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LGTM

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@maxibor maxibor left a comment

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A few minor comments to address, but otherwise, the great reset seems to be fine ;)

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@jfy133 jfy133 merged commit 6c0c9d5 into master Mar 24, 2022
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3 participants