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Published 20 hours ago • verified publisher icon nf-core

update MultiQC report

Open jfy133 opened this issue 3 years ago • 3 comments
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This updates the MultiQC config

  • Only scans for tools that are used in the pipeline
  • Adds the nf-core/mag logo to the report
  • Reorders so bowtie2 output comes before QUAST (note this may be incorrect at the moment, as it should display the custom_data host_removal thing)

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/mag 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).
  • [ ] 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).

jfy133 avatar Jun 01 '22 13:06 jfy133

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

Posted for pipeline commit 268ad30

+| ✅ 158 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

:grey_question: Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-23 12:32:16

github-actions[bot] avatar Jun 01 '22 13:06 github-actions[bot]

In this context the issue https://github.com/nf-core/mag/issues/311 (Bowtie2 assembly section missing when host read removal is turned on) could be addressed as well. And a custom description about the Bowtie2 assembly section would be nice (so far it is not clear what this plot is showing, not sure if this was lost at some point).

skrakau avatar Jun 01 '22 15:06 skrakau

Consider adding BCFtools for the aDNA subworkflow.

skrakau avatar Jun 08 '22 09:06 skrakau

MultiQC Supported Tools:

  • [x] fastqc [in]
  • [x] fastp [in]
  • [x] adapterremoval [nt]
  • [x] bowtie2 [in - check host removal]
  • [x] kraken2 [in]
  • [x] centrifuge [in]
  • [ ] porechop (local module not supported)
  • [ ] filtlong (local module not supported)
  • [ ] ~bcftools~ EDIT: supported stats command not in pipeline, not necessary after speaking with Alex
  • [x] busco [in]
  • [x] quast [in]
  • [x] prokka [in]

jfy133 avatar May 11 '23 10:05 jfy133

I started to refactor th ewhole MultiQC passing as it was rather complicated.

Next steps:

  • [x] 'Duplciate' the If/else statements around the mixing calls at the end (the mixing does have to be at teh end of the script right before MQC for some reason I don't understand)
  • [x] Add the missing tools to the channel
  • [x] Review the structure of the multiqc_config so it a) has all expected samples b) in right order

jfy133 avatar May 11 '23 11:05 jfy133

Currently not working, only prokka results being shown

jfy133 avatar Jun 13 '23 08:06 jfy133

Should work now! TODO:

  • [x] Check when all modules run (to also review order)
    • [x] Checjk ADapterRemoval
  • [x] Fix prokka custom setting due to :+1:
  • [x] methods description
  • [x] Table order

image

Example:

multiqc.zip

jfy133 avatar Jun 13 '23 17:06 jfy133

  • [x] Last thing to do: check ordering of General Stats Table

jfy133 avatar Jun 15 '23 11:06 jfy133

multiqc_report.zip

Proof of AR2 support

jfy133 avatar Jun 15 '23 14:06 jfy133

@nf-core-bot fix linting

jfy133 avatar Jun 15 '23 21:06 jfy133

mag_mqc_report2.zip

jfy133 avatar Jun 15 '23 21:06 jfy133

@d4straub found the issue, 8 mappings against assembly should be seen now :)

jfy133 avatar Jun 23 '23 12:06 jfy133