Fix for issue #201 #208 #202

apeltzer · 2022-10-27T09:38:01Z

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/smrnaseq 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).

github-actions · 2022-10-27T09:40:05Z

`nf-core lint` overall result: Passed ✅

Posted for pipeline commit aa7ea9a

+| ✅ 158 tests passed       |+

✅ Tests passed:

files_exist - File found: .gitattributes
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files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.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
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files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
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files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
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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
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files_exist - File found: assets/nf-core-smrnaseq_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-smrnaseq_logo_light.png
files_exist - File found: docs/images/nf-core-smrnaseq_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
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files_exist - File found: docs/usage.md
files_exist - File found: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreSchema.groovy
files_exist - File found: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
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files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowSmrnaseq.groovy
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files_exist - File not found check: Singularity
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files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
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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/Workflow.groovy
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
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: manifest.homePage
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.show_hidden_params
nextflow_config - Config variable found: params.schema_ignore_params
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 manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: '2.1.1dev'
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
files_unchanged - .gitattributes matches the template
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files_unchanged - .github/workflows/branch.yml matches the template
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files_unchanged - .github/workflows/linting.yml matches the template
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files_unchanged - assets/nf-core-smrnaseq_logo_light.png matches the template
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files_unchanged - docs/images/nf-core-smrnaseq_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreSchema.groovy matches the template
files_unchanged - lib/NfcoreTemplate.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml 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 Nextflow minimum version badge matched config. Badge: 22.10.1, Config: 22.10.1
readme - README Nextflow minimum version in Quick Start section matched config. README: 22.10.1, Config: 22.10.1
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (122 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.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' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.7.2
Run at 2023-02-17 22:02:14

apeltzer · 2022-10-28T08:24:21Z

That fixes that issue, but not the edgeR-QC one.

Important! Template update for nf-core/tools v2.7.2

conf/modules.config

nextflow.config

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>

sean-at-tessera · 2023-02-17T20:28:11Z

@apeltzer I think the edgeR-QC bug is here. If data only has one column, it will lose its dimensionality and the subsequent colSums() will fail. Changing this line to
data<-data[!row_sub,, drop=FALSE]
fixes this issue in my local testing.

apeltzer · 2023-02-17T21:31:11Z

Good spot, will replace this. Just didn't have the time anymore to search for the particular issue where it fails, but this looks good 👍🏻

@sean-at-tessera

Co-authored-by: Sean Corbett @sean-at-tessera

apeltzer · 2023-02-17T21:49:26Z

Also looks like tests are passing one after each other - thank you @sean-at-tessera !

[FIX] Skip_qc not being used #208

FriederikeHanssen · 2023-02-18T10:04:31Z

LICENSE

@@ -1,6 +1,6 @@
 MIT License

-Copyright (c) P. Ewels, C. Wang, R. Hammarén, L. Pantano
+Copyright (c) P. Ewels, C. Wang, R. Hammarén, L. Pantano, A. Peltzer


You are missing in the Credits section in the readme :)

FriederikeHanssen

🚀

Fix for issue #201

021dcb2

apeltzer enabled auto-merge October 27, 2022 09:38

apeltzer and others added 10 commits December 2, 2022 14:05

FIXES 208

ae02a76

Fix changelog prettier

8eac40a

Template update for nf-core/tools version 2.7.1

2e0fc78

Template update for nf-core/tools version 2.7.2

e29f9cc

Merge branch 'fix-201' into nf-core-template-merge-2.7.2

9d58af4

Update modules

65d04a4

Fix prettier

bb8c603

Fix black

bba8149

Merge pull request #217 from nf-core/nf-core-template-merge-2.7.2

244c1f6

Important! Template update for nf-core/tools v2.7.2

Merge branch 'dev' into fix-201

452a8de

maxulysse reviewed Feb 7, 2023

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maxulysse reviewed Feb 7, 2023

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apeltzer and others added 3 commits February 7, 2023 20:36

Fix Conda directives

c3a4201

Apply suggestions from code review

33de978

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>

Redid licence, to match lint

f81ddb4

apeltzer requested review from maxulysse, christopher-mohr and JoseEspinosa February 7, 2023 20:45

apeltzer added 2 commits February 17, 2023 22:36

Fix for edgeR QC

8810b08

Co-authored-by: Sean Corbett @sean-at-tessera

Merge branch 'dev' into fix-208-skip-qc

f25093f

apeltzer added 2 commits February 17, 2023 22:59

Merge branch 'fix-201' into fix-208-skip-qc

e7db15f

Merge pull request #210 from nf-core/fix-208-skip-qc

aa7ea9a

[FIX] Skip_qc not being used #208

apeltzer changed the title ~~Fix for issue #201~~ Fix for issue #201 #208 Feb 17, 2023

apeltzer mentioned this pull request Feb 17, 2023

SkipQC parameter not being used #208

Closed

FriederikeHanssen reviewed Feb 18, 2023

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FriederikeHanssen approved these changes Feb 18, 2023

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apeltzer merged commit 28a55ec into dev Feb 18, 2023

apeltzer deleted the fix-201 branch February 21, 2023 12:31

sean-at-tessera mentioned this pull request Apr 7, 2023

[Feat] Add UMI Handling to the pipeline #164

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Fix for issue #201 #208 #202

Fix for issue #201 #208 #202

apeltzer commented Oct 27, 2022

github-actions bot commented Oct 27, 2022 •

edited

✅ Tests passed:

Run details

apeltzer commented Oct 28, 2022

sean-at-tessera commented Feb 17, 2023

apeltzer commented Feb 17, 2023

apeltzer commented Feb 17, 2023

FriederikeHanssen Feb 18, 2023

FriederikeHanssen left a comment

Fix for issue #201 #208 #202

Fix for issue #201 #208 #202

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apeltzer commented Oct 27, 2022

PR checklist

github-actions bot commented Oct 27, 2022 • edited

nf-core lint overall result: Passed ✅

✅ Tests passed:

Run details

apeltzer commented Oct 28, 2022

sean-at-tessera commented Feb 17, 2023

apeltzer commented Feb 17, 2023

apeltzer commented Feb 17, 2023

FriederikeHanssen Feb 18, 2023

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github-actions bot commented Oct 27, 2022 •

edited

`nf-core lint` overall result: Passed ✅