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Drop added AberrantSplicing #35

Merged
merged 18 commits into from
Aug 16, 2023
Merged

Drop added AberrantSplicing #35

merged 18 commits into from
Aug 16, 2023

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Lucpen
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@Lucpen Lucpen commented Aug 10, 2023

PR checklist

  • Drop added AberrantSplicing
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • 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).

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github-actions bot commented Aug 10, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 66284fb

+| ✅ 142 tests passed       |+
#| ❔ 139 tests were ignored |#
!| ❗  18 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in tomte.nf: Add all file path parameters for the pipeline to the list below
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-16 06:34:12

@Lucpen Lucpen marked this pull request as ready for review August 10, 2023 16:26
@Lucpen Lucpen requested a review from jemten August 10, 2023 16:34
jemten
jemten reviewed Aug 11, 2023
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Massive work Lucia! ⭐
I have some comments and questions. A lot of it has to do with variable naming, which I think could do being a little more explicit :)

bin/drop_config.py Show resolved Hide resolved
bin/drop_sample_annot.py Outdated Show resolved Hide resolved
test_data/drop_data/geneCounts_modified.tsv Outdated Show resolved Hide resolved
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subworkflows/local/analyse_transcripts.nf Outdated Show resolved Hide resolved
bin/drop_sample_annot.py Outdated Show resolved Hide resolved
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jemten
jemten reviewed Aug 15, 2023
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Looks good! Some tiny, tiny comments

bin/drop_sample_annot.py Outdated Show resolved Hide resolved
modules/local/drop_sample_annot.nf Outdated
--gtf $gtf_name \\
$baseDir/bin/drop_sample_annot.py \\
--bam ${bam} \\
--sample $input_samples \\
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Suggested change
--sample $input_samples \\
--sample ${samples.id} \\

Suggestion if you remove the check for samples

modules/local/drop_sample_annot.nf Outdated
Comment on lines 25 to 26
def strandedness = samples ? "--strandedness ${samples.strandedness}" : ""
def input_samples = samples ? "${samples.id}" : ""
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Suggested change
def strandedness = samples ? "--strandedness ${samples.strandedness}" : ""
def input_samples = samples ? "${samples.id}" : ""
def strandedness = samples ? "--strandedness ${samples.strandedness}" : ""

Maybe we should remove this part then as you here check if samples is given and otherwise sets the string to empty. See comment below . Same for strandedness if it is a mandatory parameter

Lucpen and others added 3 commits August 16, 2023 07:35
@Lucpen @jemten
Update bin/drop_sample_annot.py
9d02fe3 
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
fix drop_sample_annot.nf
f3faef8
fix drop_sample_annot.nf
66284fb
@Lucpen Lucpen requested a review from jemten August 16, 2023 07:42
jemten
jemten approved these changes Aug 16, 2023
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Looks good!

@Lucpen Lucpen merged commit 3a8a40d into master Aug 16, 2023
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@Lucpen Lucpen deleted the drop_AS branch August 16, 2023 13:01
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@Lucpen @jemten