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Replacing PROJECT_SPOTS and MCQUANT by more optimized method #15

Merged
merged 9 commits into from
Oct 25, 2023
Merged

Replacing PROJECT_SPOTS and MCQUANT by more optimized method #15

merged 9 commits into from
Oct 25, 2023

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FloWuenne
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@FloWuenne FloWuenne commented Oct 24, 2023 •
edited by kbestak
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PR checklist

The main feature of this PR is to replace the PROJECT_SPOTS and MCQUANT modules with a new module (SPOTS2CELL, temporary name). The new module needs only a fraction of the time and RAM to process the same data.

Addresses #11

  • 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 - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/molkart 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 --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 Oct 24, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 91d31bd

+| ✅ 158 tests passed       |+
!| ❗  21 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 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: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • 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 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 output.md: Write this documentation describing your workflow's output
  • 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 test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.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 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 WorkflowMolkart.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-25 13:57:38

@FloWuenne
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@kbestak : Currently still contains commented out portions for PROJECT_SPOTS and MCQUANT!

@FloWuenne FloWuenne requested a review from kbestak October 24, 2023 01:27
kbestak
kbestak approved these changes Oct 24, 2023
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I went through the code, updated some things that required changing, mainly the MultiQC break, and adding the tag for the spot2cell outputs with segmentation and added some small quality-of-life improvements (int for spot counts, rounding QC metrics). Should be ready to merge in my opinion.

@FloWuenne
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LGTM! Closes #11

@FloWuenne FloWuenne merged commit 1822788 into dev Oct 25, 2023
4 of 6 checks passed
@FloWuenne FloWuenne deleted the spot2cell branch October 25, 2023 14:14
@FloWuenne FloWuenne mentioned this pull request Oct 25, 2023
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@kbestak kbestak kbestak approved these changes

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@FloWuenne @kbestak