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Multiqc update#226

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WackerO merged 7 commits intoqbic-pipelines:devfrom
WackerO:multiqc_update
Apr 30, 2024
Merged

Multiqc update#226
WackerO merged 7 commits intoqbic-pipelines:devfrom
WackerO:multiqc_update

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@WackerO WackerO commented Feb 20, 2024 •
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This enables rnadeseq to use multiqc.zip files from newer versions of rnaseq. For an example of a report with the changes, see the attachment (the changes affect section 3 - Read mapping and assignment)

RNAseq_report_salmon.html.zip

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
  • 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 Feb 20, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 41afb06

+| ✅ 143 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗   8 tests had warnings |!
-| ❌  14 tests failed       |-
Details

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowRnadeseq.groovy
  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Config default value incorrect: params.software_versions is set as None in nextflow_schema.json but is NO_FILE6 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.genome is set as None in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.publish_dir_mode is set as copy in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.email is set as false in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.custom_config_base is set as https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version} in nextflow_schema.json but is https://raw.githubusercontent.com/nf-core/configs/master in nextflow.config.
  • nextflow_config - Config default value incorrect: params.config_profile_description is set as false in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.config_profile_contact is set as false in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.config_profile_url is set as false in nextflow_schema.json but is null in nextflow.config.
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in rnadeseq.nf: Add all file path parameters for the pipeline to the list below
  • 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
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: assets/multiqc_config.yaml
  • files_exist - File is ignored: assets/nf-core-qbic-pipelines/rnadeseq_logo_light.png
  • files_exist - File is ignored: bin/markdown_to_html.r
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_dark.png
  • files_exist - File is ignored: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_light.png
  • files_exist - File is ignored: lib/WorkflowQbic-pipelines/rnadeseq.groovy
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • nextflow_config - Config variable ignored: params.input
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: docs/README.md
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-30 06:41:29

@WackerO
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WackerO commented Feb 20, 2024

Could star_salmon also be called star_rsem in the new version?

d4straub
d4straub approved these changes Apr 29, 2024
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LGTM

Comment thread assets/RNAseq_report.Rmd
Comment thread assets/RNAseq_report.Rmd
Comment thread conf/test_star_rsem.config Outdated
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WackerO commented Apr 30, 2024

Thanks Daniel!

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d4straub commented Apr 30, 2024

Unfortunately
Can't stage file https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/QDESQ/new_rsem_multiqc.zip -- reason: Unable to access path: https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/QDESQ/new_rsem_multiqc.zip

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WackerO commented Apr 30, 2024

Unfortunately Can't stage file https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/QDESQ/new_rsem_multiqc.zip -- reason: Unable to access path: https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/QDESQ/new_rsem_multiqc.zip

That's not an issue. Those files were only uploaded in this PR, so they're not available yet. I'll merge and in the next PR they should be good to go :)

@WackerO WackerO merged commit e155229 into qbic-pipelines:dev Apr 30, 2024
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qbicStefanC commented May 2, 2024

Hi @WackerO ,
I think in principle we can release but would like to see the following adapations first:

  1. in assets/RNAseq_report.Rmd zeile 1009 + 1029: as we do not need a color code for the no of reads, change from
    ReadNumber = color_bar("lightblue")(round((ReadNumber/1000000),2)),
    #to
    ReadNumber = ReadNumber/1000000

  2. in assets/RNAseq_report.Rmd zeile 883: The intercept story only exists in the old MultiQC, so we should remove the note here in the line when the new MultiQC is read in.

  3. in assets/RNAseq_report.Rmd zeile 1039 change from
    AssignedReads = ifelse(total_assigned_tags/total_tags > 60,
    #to
    AssignedReads = ifelse((total_assigned_tags/total_tags)*100 > 60,
    #da im Report aktuell die Werte für Assigned Reads noch keine % relativ zu 100 sind.

  4. in assets/RNAseq_report.Rmd zeile 1105 change from
    Read alignment statistics {.tabset}
    #to
    Read assignment statistics {.tabset}

  5. change in assets/RNAseq_report.Rmd 1107:
    change from alignment to assignment

  6. in docs/usage.md Zeile 92 + 160 change to
    nextflow run qbic-pipelines/rnadeseq -r 2.3 -profile docker
    ###> new Release is supposed to be 2.3, not 2.2, or?

  7. For the sake of clarity, I think it would be great if you could insert an old report into the release note, and also add something like this:

"""This enables rnadeseq to use multiqc.zip files from newer versions of rnaseq (version 3.onwards). For a comparison of an old report and a new report with the changes, see the attachments (the changes affect section 3 - Read mapping and assignment). major changes are:
1) -- 3.1 Summary statistics: GC content on Trimmed and untrimmed reads was introduced
2) -- 3.3 Read assignments: No read assignment plots and stats given for newer rnaseq release based on featureCounts. Hence we left a note here
3)-- 3.5 Read strandedness: introduction of this section to infer read strandedness from RSeQC

old = "RNAseq_report.html.zip"
new = "RNAseq_report_salmon.html.zip" """

WackerO added a commit to WackerO/rnadeseq that referenced this pull request May 2, 2024
@WackerO
Fixed some things from qbic-pipelines#226
a5725c9
@WackerO WackerO mentioned this pull request May 3, 2024
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@WackerO WackerO deleted the multiqc_update branch May 28, 2024 13:36
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@WackerO @d4straub @qbicStefanC
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