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Merged
apeltzer merged 3 commits into from
Apr 1, 2021
Merged

Fix #714 #715

apeltzer merged 3 commits into from
Apr 1, 2021

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@apeltzer apeltzer commented Apr 1, 2021

Fixes the bug in nuclear contamination #714 by using fixed upstream multiqc package

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
  • 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).

@apeltzer
Update environment.yml
378596e 
Fixes the bug in nuclear contamination #714 by using fixed upstream multiqc package
@apeltzer apeltzer changed the base branch from master to dev April 1, 2021 06:44
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@apeltzer
Update CHANGELOG.md
6e269a4 
Just update changelog
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github-actions bot commented Apr 1, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b1c40d9

+| ✅ 189 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  26 tests had warnings |!
Details

❗ Test warnings:

  • conda_env_yaml - Conda dep outdated: conda-forge::python=3.7.3, 3.9.2 available
  • conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.2.2, 3.3.4 available
  • conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=7.1, 8.1.1 available
  • conda_env_yaml - Conda dep outdated: conda-forge::pygments=2.6.1, 2.8.1 available
  • conda_env_yaml - Conda dep outdated: conda-forge::openjdk=8.0.144, 11.0.9.1 available
  • conda_env_yaml - Conda dep outdated: bioconda::adapterremoval=2.3.1, 2.3.2 available
  • conda_env_yaml - Conda dep outdated: bioconda::picard=2.22.9, 2.25.1 available
  • conda_env_yaml - Conda dep outdated: bioconda::samtools=1.9, 1.12 available
  • conda_env_yaml - Conda dep outdated: bioconda::angsd=0.933, 0.935 available
  • conda_env_yaml - Conda dep outdated: bioconda::gatk4=4.1.7.0, 4.2.0.0 available
  • conda_env_yaml - Conda dep outdated: bioconda::gatk=3.5, 3.8 available
  • conda_env_yaml - Conda dep outdated: bioconda::damageprofiler=0.4.9, 1.1 available
  • conda_env_yaml - Conda dep outdated: bioconda::bedtools=2.29.2, 2.30.0 available
  • conda_env_yaml - Conda dep outdated: conda-forge::libiconv=1.15, 1.16 available
  • conda_env_yaml - Conda dep outdated: conda-forge::pigz=2.3.4, 2.6 available
  • conda_env_yaml - Conda dep outdated: bioconda::preseq=2.0.3, 3.1.2 available
  • conda_env_yaml - Conda dep outdated: bioconda::bamutil=1.0.14, 1.0.15 available
  • conda_env_yaml - Conda dep outdated: bioconda::pysam=0.15.4, 0.16.0 available
  • conda_env_yaml - Conda dep outdated: conda-forge::pandas=1.0.4, 1.2.3 available
  • conda_env_yaml - Conda dep outdated: bioconda::freebayes=1.3.2, 1.3.5 available
  • conda_env_yaml - Conda dep outdated: conda-forge::biopython=1.76, 1.78 available
  • conda_env_yaml - Conda dep outdated: conda-forge::xopen=0.9.0, 1.1.0 available
  • conda_env_yaml - Conda dep outdated: bioconda::bowtie2=2.4.1, 2.4.2 available
  • conda_env_yaml - Conda dep outdated: bioconda::mapdamage2=2.2.0, 2.2.1 available
  • conda_env_yaml - Conda dep outdated: bioconda::bbmap=38.87, 38.90 available
  • conda_env_yaml - Conda dep outdated: conda-forge::tbb=2020.2, 2021.1.1 available

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.md
  • files_unchanged - File ignored due to lint config: docs/README.md
  • files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml

✅ Tests passed:

Run details

  • nf-core/tools version 1.13.3
  • Run at 2021-04-01 06:47:26

jfy133
jfy133 approved these changes Apr 1, 2021
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Wait for tests to pass that no other new issues crops up then we merge, and I'l prep for patch release!

@ewels ewels mentioned this pull request Apr 1, 2021
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@ewels ewels linked an issue Apr 1, 2021 that may be closed by this pull request
nuclear_contamination + MultiQC #714
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3 tasks
@apeltzer apeltzer merged commit 33f1159 into dev Apr 1, 2021
@apeltzer apeltzer deleted the fix-nuc-cont branch April 1, 2021 08:51
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@jfy133 jfy133 jfy133 approved these changes

@alexandregilardet alexandregilardet Awaiting requested review from alexandregilardet

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nuclear_contamination + MultiQC

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@apeltzer @jfy133