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Nextflow duration fix#713

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apeltzer merged 5 commits intodevfrom
nextflow-duration-fix
Mar 29, 2021
Merged

Nextflow duration fix#713
apeltzer merged 5 commits intodevfrom
nextflow-duration-fix

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@jfy133 jfy133 commented Mar 26, 2021

This is a hipster fix of nf-core/tools#973, before Kevin pushes it to nf-core/tools! will skip CHANGELOG accordingly

Basically the regex in template didn't account for nextflow parsed duration values. This fixes this.

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).

@jfy133 jfy133 changed the base branch from master to dev March 26, 2021 12:10
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github-actions Bot commented Mar 26, 2021

Hi @jfy133,

It looks like this pull-request is has been made against the nf-core/eager master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/eager dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.

Thanks again for your contribution!

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github-actions Bot commented Mar 26, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit eb75b93

+| ✅ 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  • conda_env_yaml - Conda dep outdated: conda-forge::python=3.7.3, 3.9.2 available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 2021-03-26 12:19:14

@apeltzer apeltzer merged commit ebbb02b into dev Mar 29, 2021
@apeltzer apeltzer deleted the nextflow-duration-fix branch April 1, 2021 08:36
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@jfy133 @apeltzer
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