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Fix mapdamage_rescaling naming of output bam files #719

Merged
merged 4 commits into from
Apr 2, 2021
Merged

Fix mapdamage_rescaling naming of output bam files #719

merged 4 commits into from
Apr 2, 2021

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IdoBar
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@IdoBar IdoBar commented Apr 1, 2021

Use ${bam.basename} (or ${base}, which was already defined but not used) to strip the .bam extension of the original input file for the output of mapdamage_rescaling, so filenames won't turn up like this:

library_libmerged_rg_rmdup.bam_rescaled.bam

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).

IdoBar and others added 3 commits April 2, 2021 04:23
@IdoBar
Fix mapdamage_rescaling naming of output bam files
2d35145 
Use `${bam.basename}` (or `${base}`, which was already defined but not used) to strip the `.bam` extension of the original input file for the output of `mapdamage_rescaling`, so filenames won't turn up like this: 
```
library_libmerged_rg_rmdup.bam_rescaled.bam
```
@IdoBar
Merge remote-tracking branch 'nf-core/dev' into patch-6
717ba4d
@IdoBar
Updated CHANGELOG.md to reflect changes
16b4b57
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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 61e471a

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

❗ 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  • conda_env_yaml - Conda dep outdated: conda-forge::python=3.7.3, 3.9.2 available
  • conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.2.2, 3.3.4 available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 19:22:10

IdoBar
IdoBar commented Apr 1, 2021
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@jfy133
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jfy133 commented Apr 1, 2021

Just in time for a new patch release! Thank you!!

@IdoBar
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IdoBar commented Apr 2, 2021

No worries @jfy133, I have a few other ideas for improvements (which I should submit as issues), I wish I had the time/energy to stay awake for the NF hackathon and do those...
I'll just keep pushing those one by one when I get a chance.

@jfy133
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jfy133 commented Apr 2, 2021

Awesome! Feel free to bring them up in the slack channel if you want informal chat/feedback about them already

@jfy133 jfy133 merged commit 451cb05 into nf-core:dev Apr 2, 2021
@jfy133 jfy133 mentioned this pull request Apr 6, 2021
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