Pipeline summary report

tillenglert commented 1 year ago

This PR adds a report module to the nf-core/ampliseq Pipeline. The report should include short text snippets for each module and either graphs or tables depicting the output of the corresponding tool.

The report is written in Rmarkdown and is generated using an external R script using a template .Rmd file. It is still work in progress, as I first wrote everything to be working on the results directory. Currently I'm adding each individual file which is used in the report to the input of the module, R script and into the template.

This draft PR should also enable @d4straub to help me when he has some time.

(Second PR as the first one was a bit messy.)

PR checklist

[x] This comment contains a description of changes (with reason).
[x] If you've fixed a bug or added code that should be tested, add tests!
[x] 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/ampliseq branch on the nf-core/test-datasets repository.
[x] Make sure your code lints (nf-core lint).
[x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[x] Output Documentation in docs/output.md is updated.
[x] CHANGELOG.md is updated.
[x] 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 75a497b

+| ✅ 152 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 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. * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Parameter `input` is not defined in the correct subschema (input_output_options) ### :grey_question: Tests ignored: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `conf/igenomes.config` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.gitattributes` * [actions_ci](https://nf-co.re/tools-docs/lint_tests/actions_ci.html) - actions_ci ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitattributes` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitignore` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - 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'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 a matching 'report_comment'. * [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 2.9 * Run at `2023-08-11 11:11:13`

d4straub commented 1 year ago

Curiously with -profile test the DADA2 QC plots are broken but with -profile test_single they are fine. Needs to be investigated and fixed eventually!

tillenglert commented 1 year ago

https://github.com/tillenglert/ampliseq/blob/b193c0f2cddde67d4759662cb269c8c521916b52/assets/report_template.Rmd#L194 https://github.com/tillenglert/ampliseq/blob/b193c0f2cddde67d4759662cb269c8c521916b52/assets/report_template.Rmd#L195

These lines will cause issues after merging with dev (input needs to be changed to DADA2_input) corresponding to PR: https://github.com/nf-core/ampliseq/pull/569

d4straub commented 1 year ago

Now we should have all elements until and including taxonomic assignment in an ok-ish state. However, multiple testing runs need to be addressed in some way, profile test_multi can be the test case here.

tillenglert commented 1 year ago

https://github.com/BioContainers/multi-package-containers/pull/2663 The corresponding bio container should be created soon

d4straub commented 1 year ago

From my side almost all done, only add

info to docs/output
changelog
nf-test

Should only take one more coding session.

edit: the failing linting is only template update 2.9, no other issues as far as I can see.

WackerO commented 1 year ago

Regarding the report: Looks good! Two general comments:

For plots generated with plotly-compatible packages (like ggplot), the result can be made interactive within the html. This would e.g. be useful for zooming in and such. That does of course not work with the imported plots like those in 2.2 Quality Filtering
I would suggest adding at the end of the report a computational methods section where you add the versions of the different packages for better reproducibility :)

d4straub commented 1 year ago

Thanks for the review @WackerO ! About your general comments:

Right, the idea was also to produce a smaller (in MB) pdf (isnt realized yet) that can be used as email attachment, and I have no idea whether that will interfere, so the idea was to keep it simple for now. But thats a good suggestion.
Yes thats a great suggestion. However, I'd like to avoid redundancy and might just refer for software versions to the multiqc report. Probably I should also refer to non-default parameters that are listed in the multiqc report. edit: done

nf-core / ampliseq