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Add pathway analysis DB versions (3) #148

Merged
merged 8 commits into from
Sep 5, 2022
Merged

Add pathway analysis DB versions (3) #148

merged 8 commits into from
Sep 5, 2022

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WackerO
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@WackerO WackerO commented Aug 9, 2022 •
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This PR adds the versions of the databases (KEGG, REAC) used in the pathway analysis to the report as mentioned in #72 like this:
For pathway analysis, the R packages gprofiler2 v0.2.1, AnnotationDbi v1.56.1 and org.Mm.eg.db v1.56.1 were employed. Also, the following databases were queried: KEGG: KEGG FTP Release 2022-05-16, REAC: annotations: BioMart, classes: 2022-5-18.

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/rnadeseq 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).

@WackerO WackerO changed the title Add pathway analysis DB versions Add pathway analysis DB versions (3) Aug 9, 2022
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github-actions bot commented Aug 9, 2022 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 6baf913

+| ✅ 119 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗   9 tests had warnings |!
-| ❌   4 tests failed       |-

❌ Test failures:

  • files_exist - File not found: .prettierignore
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • actions_ci - '.github/workflows/ci.yml' does not check minimum NF version
  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

❗ Test warnings:

  • files_exist - File not found: pyproject.toml
  • readme - README did not have a Nextflow minimum version badge.
  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
  • 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • schema_lint - Parameter input not found in schema

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-qbic-pipelines/rnadeseq_logo_light.png
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_dark.png
  • files_exist - File is ignored: bin/markdown_to_html.r
  • files_exist - File is ignored: .github/workflows/push_dockerhub.yml
  • files_exist - File is ignored: assets/multiqc_config.yaml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • 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 2.5.1
  • Run at 2022-09-05 11:03:14

@WackerO WackerO marked this pull request as ready for review September 1, 2022 10:42
SusiJo
SusiJo reviewed Sep 2, 2022
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tests/test_batcheffect.yml Outdated
@@ -4,15 +4,15 @@
- test_batcheffect
files:
- path: results_test/differential_gene_expression/DE_genes_tables/DE_contrast_batch_b2_vs_b1.tsv
md5sum: 4c8bcede761f82803c262f28a13eb5ce
# md5sum: 4c8bcede761f82803c262f28a13eb5ce
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Why were they uncommented? Are the files suddenly not producing the same md5sums anymore?

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Yep...they changed from time to time, I am not sure when exactly this happens, I believe in different PRs the 5sums change, almost as if the github server runner changes the files...

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How do the md5sums behave when you test locally? Are they stable over multiple runs?

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Testing this right now

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I cannot make head nor tail of that...On another branch, the 5sums are still enabled and it works. Locally, I got different sums when running the same profile on cfc and thanos. I'll reenable the 5sums here. If they again don't work, I'll probably have to delete them...

SusiJo
SusiJo reviewed Sep 2, 2022
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assets/RNAseq_report.Rmd Outdated Show resolved Hide resolved
WackerO and others added 2 commits September 2, 2022 12:19
@WackerO @SusiJo
Update assets/RNAseq_report.Rmd
2fa5f36 
Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>
@WackerO
Reenabled 5sums; have to see if they work on github
6baf913
ggabernet
ggabernet approved these changes Sep 5, 2022
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Looks good to me and the md5sums seem to be fine now

@WackerO WackerO merged commit 374dee4 into qbic-pipelines:dev Sep 5, 2022
@WackerO WackerO deleted the dbversion branch September 5, 2022 12:07
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@ggabernet ggabernet ggabernet approved these changes

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3 participants
@WackerO @ggabernet @SusiJo