Release 2.6 by SusiJo · Pull Request #279 · qbic-pipelines/rnadeseq

SusiJo · 2025-06-17T14:25:13Z

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).

* add enh. volcano * update docu * add comment * rm comments, add omitNa * ch version to dev * add volcano to tests * fix deprecated key-value * update docs,changelog * prettier test rsem profile * fix contrast names

* add colors to plotly volcano * add color scale

* hotfix switch volcano colors * fix colors * add abs, rm space * rm "feature" text * update titles, legends * add subtitle for interactive plot * ch y-axis label * rm outcommented lines

* put gprofiler in tabs * revert * linting * trim whitespace * mod plot title

* raise max dimensions limit * concat ensembl ids with gene names * update changelog & usage update changelog & usage update changelog & usage Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> fix typo

* change report name * modify report * update report & tests & fix volcano colors * add to changelog, references * fix citation * fix df RIN * fix linting & ci * fix padding * update md5sums due to sampleNames * apply suggestions * update confs * apply suggestion * add num all genes * change icon * adjust docs text

* incorporate feedback * update report * fix typos * update changelog * fix pre-commit * fix spaces * fix colored cells * linting * fix typos * adjust table border * fix typos * apply suggestions * apply suggestions

* fix contrast * update usage * add to changelog * update test * PR num * ch md5sum

* adjust md5sums due to gtf biotypes * update branch * fix assignment * add biotype to final DE table * update md5sums

github-actions · 2025-06-17T14:25:22Z

This PR is against the `master` branch ❌

Do not close this PR
Click Edit and change the base to dev
This CI test will remain failed until you push a new commit

Hi @SusiJo,

It looks like this pull-request is has been made against the qbic-pipelines/rnadeseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the qbic-pipelines/rnadeseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

SusiJo · 2025-06-17T14:34:05Z

                                       ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.14.1 - https://nf-co.re
    There is a new version of nf-core/tools available! (3.3.1)


INFO     Testing pipeline: .                                                                                                                                                                                         

╭─ [?] 17 Pipeline Tests Ignored ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                                                                                   │
│ files_exist: File is ignored: lib/nfcore_external_java_deps.jar                                                                                                                                                   │
│ nextflow_config: Config variable ignored: manifest.name                                                                                                                                                           │
│ nextflow_config: Config variable ignored: manifest.homePage                                                                                                                                                       │
│ nextflow_config: Config default ignored: params.report_file                                                                                                                                                       │
│ nextflow_config: Config default ignored: params.references_file                                                                                                                                                   │
│ nextflow_config: Config default ignored: params.css                                                                                                                                                               │
│ nextflow_config: Config default ignored: params.logo                                                                                                                                                              │
│ nextflow_config: Config default ignored: params.custom_config_base                                                                                                                                                │
│ 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/PULL_REQUEST_TEMPLATE.md                                                                                                                                │
│ files_unchanged: File ignored due to lint config: .github/workflows/branch.yml                                                                                                                                    │
│ 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                                                                                                                                   │
│                                                                                                                                                                                                                   │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ [!] 3 Pipeline Test Warnings ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                                                                                   │
│ nextflow_config: Config manifest.version should end in dev: 2.6                                                                                                                                                   │
│ readme: README did not have a Nextflow minimum version badge.                                                                                                                                                     │
│ schema_lint: Parameter input is not defined in the correct subschema (input_output_options)                                                                                                                       │
│                                                                                                                                                                                                                   │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

╭─ [!] 10 Module Test Warnings ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                              ╷                                             ╷                                                                                                                                      │
│ Module name                  │ File path                                   │ Test message                                                                                                                         │
│╶─────────────────────────────┼─────────────────────────────────────────────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╴│
│ report                       │ modules/local/report.nf                     │ Unable to connect to container registry, code:  405, url: https://ghcr.io/qbic-pipelines/rnadeseq:2.6                                │
│ report                       │ modules/local/report.nf                     │ Container versions do not match                                                                                                      │
│ report                       │ modules/local/report.nf                     │ No process 'output' block found                                                                                                      │
│ samplesheet_check            │ modules/local/samplesheet_check.nf          │ Module does not emit software version                                                                                                │
│ report                       │ modules/local/report.nf                     │ Process name not used for versions.yml                                                                                               │
│ report                       │ modules/local/report.nf                     │ Missing emit statement: path "*.yml"                                                                                                 │
│ report                       │ modules/local/report.nf                     │ Missing emit statement: path "*.zip"                                                                                                 │
│ custom/dumpsoftwareversions  │ modules/nf-core/custom/dumpsoftwareversions │ New version available                                                                                                                │
│ report                       │ modules/local/report.nf                     │ Process label not specified                                                                                                          │
│ report                       │ modules/local/report.nf                     │ when: condition has been removed                                                                                                     │
│                              ╵                                             ╵                                                                                                                                      │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

╭─ [!] 3 Subworkflow Test Warnings ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                            ╷                                                ╷                                                                                                                                     │
│ Subworkflow name           │ File path                                      │ Test message                                                                                                                        │
│╶───────────────────────────┼────────────────────────────────────────────────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╴│
│ utils_nextflow_pipeline    │ subworkflows/nf-core/utils_nextflow_pipeline   │ New version available                                                                                                               │
│ utils_nfcore_pipeline      │ subworkflows/nf-core/utils_nfcore_pipeline     │ New version available                                                                                                               │
│ utils_nfvalidation_plugin  │ subworkflows/nf-core/utils_nfvalidation_plugin │ New version available                                                                                                               │
│                            ╵                                                ╵                                                                                                                                     │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY  │
├───────────────────────┤
│ [✔] 207 Tests Passed  │
│ [?]  17 Tests Ignored │
│ [!]  16 Test Warnings │
│ [✗]   0 Tests Failed  │
╰───────────────────────╯

SusiJo · 2025-06-17T14:38:07Z

Linting fails in CI due to latest nf-core tools version 3.3.1 and the pipeline here relies on nf-core tools 2.14.1

SusiJo · 2025-06-17T14:39:50Z

Branch protection could probably be fixed in the .github/workflows.branch.yml with:

[[ ${{github.event.pull_request.head.repo.full_name }} == qbic-pipelines/rnadeseq && $GITHUB_HEAD_REF == "dev" ]] || [[ $GITHUB_HEAD_REF == "patch" ]]

SusiJo · 2025-06-18T06:31:59Z

locally, the download works with nf-core tools version 2.14.1

nf-core download qbic-pipelines/rnadeseq --revision dev --outdir '.' --compress "none" --container-system 'singularity' --container-library 'quay.io' -l 'docker.io' -l 'ghcr.io' --container-cache-utilisation 'amend' --download-configuration

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.14.1 - https://nf-co.re
    There is a new version of nf-core/tools available! (3.3.1)

INFO     Saving 'qbic-pipelines/rnadeseq'                                                                                                       
          Pipeline revision: 'dev'                                                                                                              
          Use containers: 'singularity'                                                                                                         
          Container library: 'quay.io, docker.io, ghcr.io'                                                                                      
          Using $NXF_SINGULARITY_CACHEDIR': testing'                                                         
          Output directory: '.'                                                                                                      
          Include default institutional configuration: 'True'                                                                                   
INFO     Downloading centralised configs from GitHub                                                                                            
INFO     Downloading workflow files from GitHub                                                                                                 
INFO     Processing workflow revision dev, found 3 container images in total.                                                                   
Pulling singularity images ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% • 3/3 completed

CaroAMN · 2025-06-18T14:41:03Z

Linting fails in CI due to latest nf-core tools version 3.3.1 and the pipeline here relies on nf-core tools 2.14.1

I'm playing around with the CI right now for my pipeline. So what i saw in my .github/workflows/linting.yml this:

      - name: read .nf-core.yml
        uses: pietrobolcato/action-read-yaml@1.1.0
        id: read_yml
        with:
          config: ${{ github.workspace }}/.nf-core.yml

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}`
          
      which is not in your current linting.yml and i guess it checks the version in your nf-core.yml and installs the required tools version. ... maybe unnecessary but could resolve linting errors

famosab

To me this looks good but note that I am not an expert on pytests and R haha :D

github-actions · 2025-06-23T08:53:52Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit e8b4ae1

+| ✅ 170 tests passed       |+
#| ❔  18 tests were ignored |#
!| ❗   3 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.6
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:

files_exist - File is ignored: lib/nfcore_external_java_deps.jar
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
nextflow_config - Config default ignored: params.report_file
nextflow_config - Config default ignored: params.references_file
nextflow_config - Config default ignored: params.css
nextflow_config - Config default ignored: params.logo
nextflow_config - Config default ignored: params.custom_config_base
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/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.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

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-rnadeseq_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-rnadeseq_logo_light.png
files_exist - File found: docs/images/nf-core-rnadeseq_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-rnadeseq_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowRnadeseq.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.input_type= featurecounts
nextflow_config - Config default value correct: params.contrast_matrix= DEFAULT
nextflow_config - Config default value correct: params.contrast_list= DEFAULT1
nextflow_config - Config default value correct: params.contrast_pairs= DEFAULT2
nextflow_config - Config default value correct: params.genelist= NO_FILE
nextflow_config - Config default value correct: params.relevel= NO_FILE2
nextflow_config - Config default value correct: params.logFC_threshold= 0
nextflow_config - Config default value correct: params.adj_pval_threshold= 0.05
nextflow_config - Config default value correct: params.norm_method= rlog
nextflow_config - Config default value correct: params.vst_genes_number= 1000
nextflow_config - Config default value correct: params.round_DE= -1
nextflow_config - Config default value correct: params.custom_gmt= NO_FILE3
nextflow_config - Config default value correct: params.set_background= true
nextflow_config - Config default value correct: params.custom_background= NO_FILE7
nextflow_config - Config default value correct: params.min_DEG_pathway= 1
nextflow_config - Config default value correct: params.heatmaps_cluster_rows= true
nextflow_config - Config default value correct: params.heatmaps_cluster_cols= false
nextflow_config - Config default value correct: params.pathway_adj_pval_threshold= -1.0
nextflow_config - Config default value correct: params.multiqc= NO_FILE4
nextflow_config - Config default value correct: params.software_versions= NO_FILE6
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes
nextflow_config - Config default value correct: params.outdir= ./results
nextflow_config - Config default value correct: params.tracedir= ./results/pipeline_info
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - assets/email_template.html matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (174 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: push_github_container_reg.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - REPORT found in conf/modules.config and Nextflow scripts.
modules_config - SAMPLESHEET_CHECK found in conf/modules.config and Nextflow scripts.
modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2025-07-03 08:36:18

SusiJo · 2025-06-23T09:03:35Z

Linting fails in CI due to latest nf-core tools version 3.3.1 and the pipeline here relies on nf-core tools 2.14.1

I'm playing around with the CI right now for my pipeline. So what i saw in my .github/workflows/linting.yml this:

      - name: read .nf-core.yml
        uses: pietrobolcato/action-read-yaml@1.1.0
        id: read_yml
        with:
          config: ${{ github.workspace }}/.nf-core.yml

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}`
          
      which is not in your current linting.yml and i guess it checks the version in your nf-core.yml and installs the required tools version. ... maybe unnecessary but could resolve linting errors

Awesome, thanks!

SusiJo · 2025-06-23T14:42:00Z

Branch protection is failing because of a typo in the master branch which I cannot/wont fix.

rnadeseq/.github/workflows/branch.yml

Line 16 in e53bbae

    
                     "{ [[ ${{github.event.pull_request.head.repo.full_name }} == qbic-pipelines/rnadeseq ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]"

qbicStefanC · 2025-06-24T06:57:18Z

+
+The image below displays the two-step analysis workflow from your input data to differential gene expression analysis.
+In the first step, reads were aligned and assigned to genomic features using nf-core pipelines.
+In the second step, the gene counts were analyzed for differential expression with the secondary analysis pipeline rnadeseq.


we have 2x second in here, nut-picking maybe...but could be modified to : "In the next step, the resulting gene counts were analyzed for differential expression with the secondary analysis pipeline rnadeseq."

qbicStefanC · 2025-06-24T06:57:41Z

+# Workflow overview
+
+The image below displays the two-step analysis workflow from your input data to differential gene expression analysis.
+In the first step, reads were aligned and assigned to genomic features using nf-core pipelines.


"In the first step, reads were aligned and assigned to genomic features (e.g. genes) using nf-core pipelines.

qbicStefanC · 2025-06-24T07:46:21Z

-    - `Heatmaps_of_distances.pdf/.png/.svg`: heatmap of the pairwise Euclidean distances among samples, when the `r norm_method_text` normalized gene counts are considered.
-    - `PCA_plot.pdf`: PCA of the `r norm_method_text` normalized gene counts.
+- **DE_genes_tables:** folder containing one tab-separated table for each of the contrasts in the analysis. Each table contains a list of all differentially expressed genes in the contrast, specifying the mean gene expression across all samples (baseMean), and the log2 fold change value and p-adjusted values (padj) for this contrast.  If a `gtf` file is provided, the tables will also contain a column with the gene biotypes of the differentially expressed genes.
+- **final_gene_table/final_gene_list_DESeq2.tsv**: table containing a list of all genes considered in the analysis. Here a summary of the log2 Fold Change and p-adjusted values for all contrasts is displayed. Additionally, the column **filter** shows if this gene was differentially expressed (DE) in any of the contrasts, or not (not_DE). The column **contrast_vector** contains for each contrast considered in the analysis a 1 if the gene was differentially expressed for this contrast or a 0 if it was not.


I would also add this sentence here as that column is also added to the final aggregated DE table: "If a gtf file is provided, the tables will also contain a column with the gene biotypes of the differentially expressed genes."

qbicStefanC

Overall looks fine to me. Before merging let us wait for the checks on the 4 mentioned previously run projects and then see what is missing.

* fix thresholds in enhanced volcano * add to changelog

* prettify long contrast names in plot titles * add new test profile but not for ci * rename files * correct pr nums

SusiJo · 2025-06-30T09:11:48Z

Overall looks fine to me. Before merging let us wait for the checks on the 4 mentioned previously run projects and then see what is missing.

Are there any updates on the runs of the 4 projects? @qbicStefanC @MAKirch

* switch back to githubusercontent * add to changelog

SusiJo · 2025-07-03T08:35:29Z

Overall looks fine to me. Before merging let us wait for the checks on the 4 mentioned previously run projects and then see what is missing.

Are there any updates on the runs of the 4 projects? @qbicStefanC @MAKirch

Note: 4 Projects passed the tests

SusiJo added 10 commits May 5, 2025 14:52

Add EnhancedVolcano (#267)

3e7c7fb

* add enh. volcano * update docu * add comment * rm comments, add omitNa * ch version to dev * add volcano to tests * fix deprecated key-value * update docs,changelog * prettier test rsem profile * fix contrast names

Apply color scheme of EnhancedVolcano to plotly volcano (#268)

e35d203

* add colors to plotly volcano * add color scale

Hotfix colors volcano plot (#271)

e449424

* hotfix switch volcano colors * fix colors * add abs, rm space * rm "feature" text * update titles, legends * add subtitle for interactive plot * ch y-axis label * rm outcommented lines

Put gprofiler in tabs (#270)

ea98cdc

* put gprofiler in tabs * revert * linting * trim whitespace * mod plot title

Bugfixes pathway analysis (#273)

16d5e38

* raise max dimensions limit * concat ensembl ids with gene names * update changelog & usage update changelog & usage update changelog & usage Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> fix typo

Incorporate Feedback and fix typos (#276)

27d6ff9

* incorporate feedback * update report * fix typos * update changelog * fix pre-commit * fix spaces * fix colored cells * linting * fix typos * adjust table border * fix typos * apply suggestions * apply suggestions

Bugfix summary (#278)

f3613e6

* fix contrast * update usage * add to changelog * update test * PR num * ch md5sum

Add gene biotypes to interactive volcano plots (#272)

f982a8d

* adjust md5sums due to gtf biotypes * update branch * fix assignment * add biotype to final DE table * update md5sums

version bump to 2.6 (#277)

4bb671b

famosab approved these changes Jun 20, 2025

View reviewed changes

SusiJo added 2 commits June 23, 2025 08:47

update branch.yml

d9d6a4c

apply suggestion lint

d607487

add to ignore

e4b0689

SusiJo added 8 commits June 23, 2025 09:10

update branch.yml

18151b7

test docker download

d0385db

rm pull_request_target rule

04292cd

update branch protection

33e7a5a

update branch protection

4315c41

update branch protection

5fb0c46

revert branch yml

82d9663

update branch yml

3f131d1

SusiJo added 2 commits June 24, 2025 06:34

test download

8725eae

test update

b67606f

qbicStefanC reviewed Jun 24, 2025

View reviewed changes

SusiJo added 2 commits June 24, 2025 07:56

update branch.yml

1dc3b25

change publishdir mode

89837d2

qbicStefanC approved these changes Jun 24, 2025

View reviewed changes

SusiJo added 12 commits June 24, 2025 09:08

update version test

80490f5

Bugfix volcano (#280)

a05596e

* fix thresholds in enhanced volcano * add to changelog

Prettify long contrast names in plot titles (#281)

1aab4a4

* prettify long contrast names in plot titles * add new test profile but not for ci * rename files * correct pr nums

apply suggestions (#282)

5ca86a6

update env name

c9d0e31

revert download.yml

5688d48

test apptainer

1e8a553

change order

a711c8d

revert download.yml

a8734eb

Merge remote-tracking branch 'refs/remotes/origin/dev' into dev

5ba203a

revert cachedir

f35d74f

update md5sum

c3a03b3

Modify input base (#283)

e8b4ae1

* switch back to githubusercontent * add to changelog

SusiJo merged commit 1311f0b into master Jul 3, 2025
36 of 37 checks passed

Conversation

SusiJo commented Jun 17, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

PR checklist

Uh oh!

github-actions Bot commented Jun 17, 2025

This PR is against the master branch ❌

Uh oh!

SusiJo commented Jun 17, 2025

Uh oh!

SusiJo commented Jun 17, 2025

Uh oh!

SusiJo commented Jun 17, 2025

Uh oh!

SusiJo commented Jun 18, 2025

Uh oh!

CaroAMN commented Jun 18, 2025 • edited by famosab Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

famosab left a comment

Choose a reason for hiding this comment

Uh oh!

github-actions Bot commented Jun 23, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

SusiJo commented Jun 23, 2025

Uh oh!

SusiJo commented Jun 23, 2025

Uh oh!

qbicStefanC Jun 24, 2025

Choose a reason for hiding this comment

Uh oh!

qbicStefanC Jun 24, 2025

Choose a reason for hiding this comment

Uh oh!

qbicStefanC Jun 24, 2025

Choose a reason for hiding this comment

Uh oh!

qbicStefanC left a comment

Choose a reason for hiding this comment

Uh oh!

SusiJo commented Jun 30, 2025

Uh oh!

SusiJo commented Jul 3, 2025

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

SusiJo commented Jun 17, 2025 •

edited

Loading

This PR is against the `master` branch ❌

CaroAMN commented Jun 18, 2025 •

edited by famosab

Loading

github-actions Bot commented Jun 23, 2025 •

edited

Loading

`nf-core lint` overall result: Passed ✅ ⚠️