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Fix condition preventing to run multivcfanalyzer #711

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Merged
jfy133 merged 6 commits into from
Mar 29, 2021
Merged

Fix condition preventing to run multivcfanalyzer #711

jfy133 merged 6 commits into from
Mar 29, 2021

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@maxibor
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@maxibor maxibor commented Mar 24, 2021

A bit of cleanup and fixing a parameter type to allow to run MultiVCFAnalyzer

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!
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • CHANGELOG.md is updated.

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maxibor commented Mar 25, 2021

Merged dev branch back into PR branch to sync with template update @jfy133

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github-actions bot commented Mar 25, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d11de6a

+| ✅ 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  • conda_env_yaml - Conda dep outdated: conda-forge::python=3.7.3, 3.9.2 available
  • conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.2.2, 3.3.4 available
  • conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=7.1, 8.1.1 available
  • conda_env_yaml - Conda dep outdated: conda-forge::pygments=2.6.1, 2.8.1 available
  • conda_env_yaml - Conda dep outdated: conda-forge::openjdk=8.0.144, 11.0.9.1 available
  • conda_env_yaml - Conda dep outdated: bioconda::adapterremoval=2.3.1, 2.3.2 available
  • conda_env_yaml - Conda dep outdated: bioconda::picard=2.22.9, 2.25.1 available
  • conda_env_yaml - Conda dep outdated: bioconda::samtools=1.9, 1.12 available
  • conda_env_yaml - Conda dep outdated: bioconda::angsd=0.933, 0.935 available
  • conda_env_yaml - Conda dep outdated: bioconda::gatk4=4.1.7.0, 4.2.0.0 available
  • conda_env_yaml - Conda dep outdated: bioconda::gatk=3.5, 3.8 available
  • conda_env_yaml - Conda dep outdated: bioconda::damageprofiler=0.4.9, 1.1 available
  • conda_env_yaml - Conda dep outdated: bioconda::bedtools=2.29.2, 2.30.0 available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 1.13.2
  • Run at 2021-03-25 13:31:34

jfy133
jfy133 reviewed Mar 25, 2021
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jfy133
jfy133 requested changes Mar 25, 2021
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LGTM, just need a CHANGELOG update and good to go

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maxibor commented Mar 26, 2021

Changelog updated @jfy133

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jfy133 commented Mar 26, 2021

Fix markdown lint and you can merge @maxibor! (ignore nf-core linting issue)

@jfy133 jfy133 merged commit 6532e74 into nf-core:dev Mar 29, 2021
@jfy133 jfy133 mentioned this pull request Apr 6, 2021
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@maxibor @jfy133