Thanks to visit codestin.com
Credit goes to github.com

Skip to content

Fix mapdamage_rescaling naming of output bam files #719

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
jfy133 merged 4 commits into from
Apr 2, 2021
Merged

Fix mapdamage_rescaling naming of output bam files #719

jfy133 merged 4 commits into from
Apr 2, 2021

Conversation

@IdoBar
Copy link
Contributor

@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
@github-actions
Copy link

github-actions bot commented Apr 1, 2021 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 61e471a

+| ✅ 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 19:22:10

IdoBar
IdoBar commented Apr 1, 2021
View reviewed changes
@jfy133
Copy link
Member

jfy133 commented Apr 1, 2021

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

@IdoBar
Copy link
Contributor Author

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
Copy link
Member

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
Merged
11 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@jfy133 jfy133 jfy133 approved these changes

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@IdoBar @jfy133