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Pipeline summary report #558

Merged
merged 100 commits into from
Aug 11, 2023
Merged

Pipeline summary report #558

merged 100 commits into from
Aug 11, 2023

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tillenglert
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@tillenglert tillenglert commented Mar 24, 2023 •
edited by d4straub
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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

  • 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/ampliseq 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 Mar 24, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 75a497b

+| ✅ 152 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-11 11:11:13

@d4straub d4straub changed the title Initial commit for draft PR HTML Summary report Mar 24, 2023
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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!

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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: #569

tillenglert
tillenglert commented Aug 4, 2023
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Some comments already

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assets/report_template.Rmd
max_disc <- round( 100 - min(passed_col), 1 )
avg_passed <- round(mean(passed_col),1)

cutadapt_text_unch <- "Primers were trimmed using cutadapt"
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Maybe this sentence can be omitted if the flag retain untrimmed is set.

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@d4straub d4straub Aug 4, 2023 •
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I would argue that even if untrimmed are retained, the trimming was attempted and therefore that text snippet is fine I think.

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@d4straub d4straub changed the title HTML Summary report Pipeline summary report Aug 8, 2023
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d4straub approved these changes Aug 11, 2023
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Approving here. Code was written by 2 devs and reviewed by a third.
The product of that addition, the pipeline summary report itself, was also reviewed several times by multiple people. While its never finished, it seems in a good state to be added to the pipeline imho.

@d4straub d4straub merged commit c801a21 into nf-core:dev Aug 11, 2023
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