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Merged
apeltzer merged 9 commits into from
Mar 29, 2021
Merged

Pmdtools extension #708

apeltzer merged 9 commits into from
Mar 29, 2021

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@TCLamnidis
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@TCLamnidis TCLamnidis commented Mar 22, 2021

Added pmdtools_platypus option (boolean). When activated the --platypus option is passed to pmdtools, and an extended base misincorporation frequency table is appended to the misincorporation estimates file.

Issues linked to this PR:
#349

PR checklist

  • This comment contains a description of changes (with reason).
  • 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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github-actions bot commented Mar 22, 2021

Hi @TCLamnidis,

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!

@TCLamnidis TCLamnidis changed the base branch from master to dev March 22, 2021 13:40
@TCLamnidis TCLamnidis linked an issue Mar 22, 2021 that may be closed by this pull request
Add --platypus option to PMDtools #349
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@TCLamnidis
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TCLamnidis commented Mar 22, 2021

I suspect #706 needs merging before the linting issues will be resolved.

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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 f374ed2

+| ✅ 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  • conda_env_yaml - Conda dep outdated: conda-forge::python=3.7.3, 3.9.2 available
  • conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.2.2, 3.3.4 available
  • conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=7.1, 8.1.1 available
  • conda_env_yaml - Conda dep outdated: conda-forge::pygments=2.6.1, 2.8.1 available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 2021-03-29 08:17:04

@nf-core nf-core deleted a comment from github-actions bot Mar 25, 2021
jfy133
jfy133 reviewed Mar 25, 2021
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Small request on CHANGELOG otherwise looks good to me. Could also add it to the CI tests if you think would be worth it

TCLamnidis and others added 2 commits March 26, 2021 16:06
@TCLamnidis
Added link to issue
7616494
@apeltzer
Update Dockerfile
f374ed2 
Fix Dockerfile to make linter pass
@jfy133 jfy133 self-requested a review March 29, 2021 09:44
@apeltzer apeltzer merged commit 552d35b into dev Mar 29, 2021
@apeltzer apeltzer deleted the pmdtools-extension branch March 29, 2021 15:44
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Add --platypus option to PMDtools

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@TCLamnidis @jfy133 @apeltzer