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Implementation of IsoformSwitchAnalyzeR #142

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Implementation of IsoformSwitchAnalyzeR #142

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jesseangelis
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@jesseangelis jesseangelis commented Jun 6, 2024 •
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Description of changes

In reference to issue #148

Dear rnasplice team, as my colleague discussed with you on slack on 15 February, I have added IsoformSwitchAnalyseR to the pipeline.

IsoformSwitchAnalyzeR is a powerful tool for identifying isoform switches in transcript data.

IsoformSwitchAnalyzeR takes a Salmon results directory as input. If it finds genes with isoform switches, it produces publication-quality plots visualising these switches. A separate set of switch plots is generated for each contrast if that contrast contains significant switches. Two .csv files are also created, a summary and the main data frame. The .rds of the main R-list is also returned.
This results in the following file structure:

isoformswitchanalyzer
|-- results
| |-- Condition1_vs_Condition2
| | |-- 01_switch_plot_gene1.pdf
| | |-- 02_switch_plot_gene2.pdf
| | |-- 03_switch_plot_gene3.pdf
| |
| |-- Condition2_vs_Condition3
| | |-- 01_switch_plot_gene4.pdf
| | |-- 02_switch_plot_gene5.pdf
| | |-- 03_switch_plot_gene6.pdf
|
|-- isoformswitchanalyzer_isoformfeatures.csv
|
|-- isoformswitchanalyzer_summary.csv
|
|-- switchlist.rds

Details

A new local module was added calling an R script in bin.
The module is called from the rnasplice workflow.
A new test for IsoformSwitchAnalyzeR was added.
Documentation, config scripts, etc. were updated according to the guidelines.

Some of the commits are from merges with the updated master branch.

The lint checks failed. But they also failed before I implemented the changes.

PR checklist

  • This comment contains a description of changes (with reason).
  • 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

jma1991 and others added 18 commits November 16, 2023 13:38
@jma1991
Merge pull request nf-core#103 from nf-core/dev
907c293 
Patch v1.0.1
@jma1991
Merge pull request nf-core#116 from nf-core/dev
f70bbce 
Release of patch fix v1.0.2
@jma1991
Merge pull request nf-core#125 from nf-core/dev
2b7adfa 
Patch fix v1.0.3
@jma1991
Fix incorrect assignment of cluster groups
647c95b
@jma1991
Update CHANGELOG
e5ee51e
@jma1991
Merge pull request nf-core#132 from jma1991/patch
1d0494a 
Fix incorrect assignment of cluster groups
@jesseangelis
Add IsoformSwitchAnalyzeR to pipeline
57db8c4
@jesseangelis
Update json files and and config
e6ece86
@jesseangelis
Add IsoformSwitchAnalyzeR test
a989f17
@jesseangelis
Update documentation
c45dc42
@jesseangelis
Resolve commit conflicts
e831da5
@jesseangelis
Resolve missing output if no switches were found
4253946
@jesseangelis
Update Credits
1baebfe
@jesseangelis
Update Docs
aa375af
@jesseangelis
Format using prettier
996d9f7
@jesseangelis
Update output documentation
f285915
@jesseangelis
Format output documentation
1f4bd68
@jesseangelis
Update dIF definition
dad7ffd
@jesseangelis jesseangelis changed the title Dev Implementation of IsoformSwitchAnalyzeR Jun 6, 2024
@jma1991 jma1991 requested review from jma1991, bensouthgate and lathikaa and removed request for jma1991 August 21, 2024 18:32
@jma1991
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jma1991 commented Aug 21, 2024

Hi Jesse,

Thank you so much for submitting a pull request for IsoformSwitchAnalyzerR!

I’ve added myself along with two other maintainers to help review it.

@bensouthgate, if you’ve got a moment, could you take a look?
@lathikaa, could you or someone from the bioinformatics team also give it a review when possible?

Thanks again for your contribution!

Best regards,
James

@jma1991
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jma1991 commented Aug 21, 2024

@lathikaa Can you also replicate the changes to the metro-map which Jesse has committed using the original Canva template?

@jesseangelis
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@bensouthgate
@lathikaa
@jma1991

Hi everyone, the code review has been pending for a while now. Is there anything I can help you with to get it started?
Best regard,
Jesse

@lathikaa
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lathikaa commented Oct 22, 2024 •
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Hi @jesseangelis ,
Apologies for the delay. We've tested the code, and everything is looking good so far. Just a few final steps and the metro map need to be updated. We'll have it merged soon. Sorry that it's taking a bit longer than expected, but we're almost there!

Thanks,
Lathika

@jesseangelis
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@lathikaa
Sounds good! Is there anything I can help you with?

@lathikaa
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@jesseangelis We need to make updates to remove the lib folder to ensure that nf-core linting passes, enabling us to merge into the dev branch. We're currently reviewing the necessary changes to accomplish this.

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github-actions bot commented Oct 31, 2024 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 7457cc7

+| ✅ 259 tests passed       |+
!| ❗   6 tests had warnings |!
-| ❌  20 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/WorkflowRnasplice.groovy
  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Config variable (incorrectly) found: params.max_cpus
  • nextflow_config - Config variable (incorrectly) found: params.max_memory
  • nextflow_config - Config variable (incorrectly) found: params.max_time
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/email_template.html does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • files_unchanged - assets/nf-core-rnasplice_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-rnasplice_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-rnasplice_logo_dark.png does not match the template
  • files_unchanged - .gitignore does not match the template
  • actions_awsfulltest - .github/workflows/awsfulltest.yml is not triggered correctly

❗ Test warnings:

  • files_exist - File not found: conf/igenomes_ignored.config
  • nextflow_config - Config manifest.version should end in dev: 1.0.5
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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 WorkflowRnasplice.groovy: Optionally add in-text citation tools to this list.
  • nfcore_yml - nf-core version not set in .nf-core.yml

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-31 16:58:44

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Reviewers

@lathikaa lathikaa lathikaa approved these changes

@bensouthgate bensouthgate Awaiting requested review from bensouthgate

@jma1991 jma1991 Awaiting requested review from jma1991

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3 participants
@jesseangelis @jma1991 @lathikaa