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Add palom as local module #50

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gesavoigt
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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 - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/mcmicro 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>).
  • 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).

Note: test & debug runs included default segmentation option ashlar, not palom

Description of module specifications

For mcmicro, palom can be used to register pre-stitched images instead of ashlar.

The module as implemented here calls the script align_multiple_cycles.py. The script is currently not integrated in the original palom repository, but a PR is opened by @kbestak. After it has been accepted, the next steps would be to update the pip package, create a new docker, and create an nf-core module (with the function being called through the package).

Note also that no license has been provided in the palom GitHub repo. An MIT license it expected to be added, an issue has been opened.

Description of changes

  • nextflow.config:
    • added pipeline param registration_method to choose between ashlar (default) and palom
    • added module param palom_align_channel to specify channel to use for image registration with palom
  • nextflow_schema.json:
    • Reflects changes made to nextflow.config
  • conf/modules.config:
    • based on params.registration_method, ashlar or palom can be executed
    • param.palom_align_channel is an optional parameter to specify the imaging channel used for alignment
  • workflows/mcmicro.nf:
    • modify ch_registration for compatibility with both ashlar and palom
    • for palom, ch_registration combines all files with the same meta id to be registered into one image
  • modules/local/palom/alignmultiplecycles/:
    • Implementation of the module as described above.

@github-actions GitHub Actions
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github-actions bot commented Aug 8, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0ef3266

+| ✅ 181 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  25 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.0.0
  • 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: TODO nf-core:
  • 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 main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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 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 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 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 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
  • schema_lint - Parameter input not found in schema

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-08 07:59:44

@gesavoigt
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Update: An MIT license has been added to labsyspharm/palom

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@gesavoigt