Added logic for transformation method

WackerO commented 1 year ago

This PR adds a threshold for size factor variance (0.05) above which the pipeline will automatically use rlog transformation even if the user requests vst (can be overridden by user). Additionally, heatmaps are now saved inside a trycatch (especially png() often throws an error), meanSdPlot has now correct plot titles depending on rlog/vst and < or > comparisons (is pval < 0.05) are now always <= or >= (is pval <= 0.05) as this is also what the gost() function does.

@qbicStefanC

PR checklist

[x] 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/rnadeseq branch on the nf-core/test-datasets repository.
[ ] Make sure your code lints (nf-core lint).
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[x] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[x] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).

github-actions[bot] commented 1 year ago

`nf-core lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 646ffa4

+| ✅ 125 tests passed       |+
#| ❔  27 tests were ignored |#
!| ❗  10 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README did not have a Nextflow minimum version badge. * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `methods_description_template.yml`: _#Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `rnadeseq.nf`: _Add all file path parameters for the pipeline to the list below_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `WorkflowMain.groovy`: _Add Zenodo DOI for pipeline after first release_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `base.config`: _Check the defaults for all processes_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `base.config`: _Customise requirements for specific processes._ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - 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Config variable found: `timeline.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `trace.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `report.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `dag.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.cpus` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.memory` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.time` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.outdir` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.show_hidden_params` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - 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Workflow validation passed: branch.yml * [merge_markers](https://nf-co.re/tools-docs/lint_tests/merge_markers.html) - No merge markers found in pipeline files * [modules_json](https://nf-co.re/tools-docs/lint_tests/modules_json.html) - Only installed modules found in `modules.json` * [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins. * [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains 'export_plots: true'. * [modules_structure](https://nf-co.re/tools-docs/lint_tests/modules_structure.html) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL' ### Run details * nf-core/tools version 2.8 * Run at `2023-06-20 11:38:05`

SusiJo commented 1 year ago

If you are changing the parameter name of pval_threshold please also update the docs.

WackerO commented 1 year ago

If you are changing the parameter name of pval_threshold please also update the docs.

Param is now called adj_pval_threshold and this is reflected in usage.md, I assume that is what you meant? I'll ask @qbicStefanC about the renaming and if necessary do a follow-up PR to rename it back to pval_threshold

qbic-pipelines / rnadeseq