Adding fluteMLE and day0 #126

LaurenceKuhl · 2024-03-18T12:40:41Z

PR checklist

…to mageckFlute

github-actions · 2024-03-18T12:42:35Z

`nf-core lint` overall result: Failed ❌

Posted for pipeline commit 1858b5e

+| ✅ 169 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   2 tests had warnings |!
-| ❌  10 tests failed       |-

❌ 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/WorkflowCrisprseq.groovy
files_unchanged - .github/CONTRIBUTING.md does not match the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
files_unchanged - .github/workflows/branch.yml does not match the template
files_unchanged - .github/workflows/linting_comment.yml does not match the template
files_unchanged - .github/workflows/linting.yml does not match the template
files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

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
pipeline_todos - TODO string in WorkflowCrisprseq.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

files_exist - File is ignored: conf/test.config
files_exist - File is ignored: conf/test_full.config

✅ 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-crisprseq_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: docs/images/nf-core-crisprseq_logo_light.png
files_exist - File found: docs/images/nf-core-crisprseq_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 found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: .nf-core.yaml
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: .github/workflows/push_dockerhub.yml
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: docs/images/nf-core-crisprseq_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
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: lib/nfcore_external_java_deps.jar
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.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 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: 2.2.0dev
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.umi_bin_size= 1
nextflow_config - Config default value correct: params.medaka_model= r941_min_high_g303
nextflow_config - Config default value correct: params.aligner= minimap2
nextflow_config - Config default value correct: params.vsearch_minseqlength= 55
nextflow_config - Config default value correct: params.vsearch_maxseqlength= 57
nextflow_config - Config default value correct: params.vsearch_id= 0.99
nextflow_config - Config default value correct: params.min_reads= 30.0
nextflow_config - Config default value correct: params.min_targeted_genes= 3.0
nextflow_config - Config default value correct: params.bagel_reference_essentials= https://raw.githubusercontent.com/hart-lab/bagel/master/CEGv2.txt
nextflow_config - Config default value correct: params.bagel_reference_nonessentials= https://raw.githubusercontent.com/hart-lab/bagel/master/NEGv1.txt
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/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
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.validationSchemaIgnoreParams= genomes,igenomes_base
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-crisprseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-crisprseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-crisprseq_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore 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: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (217 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
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awsfulltest_screening.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: download_pipeline.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' 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 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 2.13.1
Run at 2024-03-21 10:32:15

… day0

CHANGELOG.md

conf/modules.config

templates/template_fluteMLE.R

workflows/crisprseq_screening.nf

Co-authored-by: Matthias Hörtenhuber <[email protected]>

LaurenceKuhl added 10 commits February 15, 2024 16:05

Add mageckFlute

d2053cd

Merge branch 'master' of https://github.com/LaurenceKuhl/crisprseq in…

f267891

…to mageckFlute

Merge remote-tracking branch 'upstream/dev' into mageckFlute

1665934

Merge branch 'dev' of https://github.com/nf-core/crisprseq into day0

20f725c

Adding day0 as an option for the user

df02816

add fluteMLE

c66c1ef

Adding day 0 and fluteMLE

4aa4ffa

Fix commit merges

138ef01

Add day0 in fluteMLE

1fee89a

Fix typo in fluteMLE

2e87fd4

LaurenceKuhl added 7 commits March 18, 2024 13:50

Remove prints

e2c5501

Fix day0 and fluteMLE

81c83e4

Add day0 label, fix mageck MLE and add fluteMLE

137b1af

run pre commit and prettier

ce0ea51

Delete modules/local/mageckflute.nf

5549383

finish doc

62facd2

Merge branch 'day0' of https://github.com/LaurenceKuhl/crisprseq into…

dc95c5e

… day0

mashehu approved these changes Mar 21, 2024

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conf/modules.config Outdated Show resolved Hide resolved

templates/template_fluteMLE.R Show resolved Hide resolved

workflows/crisprseq_screening.nf Outdated Show resolved Hide resolved

LaurenceKuhl and others added 5 commits March 21, 2024 11:22

Update workflows/crisprseq_screening.nf

9bab82c

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Update CHANGELOG.md

fde49d5

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Update conf/modules.config

442d5f3

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Add version of clusterprofiler

3498ec0

Add version of clusterprofiler

1858b5e

LaurenceKuhl merged commit c35c283 into nf-core:dev Mar 21, 2024

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Adding fluteMLE and day0 #126

Adding fluteMLE and day0 #126

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LaurenceKuhl commented Mar 18, 2024

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github-actions bot commented Mar 18, 2024 •

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Adding fluteMLE and day0 #126

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LaurenceKuhl commented Mar 18, 2024

PR checklist

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nf-core lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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github-actions bot commented Mar 18, 2024 •

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`nf-core lint` overall result: Failed ❌