3.2.2 Release Candidiate #230

chris-cheshire · 2024-02-01T11:33:05Z

[3.2.2] - 2024-02-01

Enhancements

Updated pipeline template to nf-core/tools 2.12.
Added option to dump calculated scale factor values from the pipeline using --dump_scale_factors
Added options to group IGV tracks by samplesheet group or by file type using --igv_sort_by_groups

Fixes

Fixed error that caused mismapping of IgG controls to their targets in certain samplesheet configurations.

…to template-merge

Updates

github-actions · 2024-02-01T11:42:39Z

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

Posted for pipeline commit f1b7994

+| ✅ 205 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 3.2.2
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 WorkflowCutandrun.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt

✅ 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-cutandrun_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-cutandrun_logo_light.png
files_exist - File found: docs/images/nf-core-cutandrun_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: 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
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: lib/WorkflowCutandrun.groovy
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-cutandrun_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 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.outdir= ./results
nextflow_config - Config default value correct: params.spikein_genome= K12-MG1655
nextflow_config - Config default value correct: params.clip_r1= 0
nextflow_config - Config default value correct: params.clip_r2= 0
nextflow_config - Config default value correct: params.three_prime_clip_r1= 0
nextflow_config - Config default value correct: params.three_prime_clip_r2= 0
nextflow_config - Config default value correct: params.trim_nextseq= 0
nextflow_config - Config default value correct: params.aligner= bowtie2
nextflow_config - Config default value correct: params.normalisation_c= 10000
nextflow_config - Config default value correct: params.minimum_alignment_q_score= 20
nextflow_config - Config default value correct: params.end_to_end= true
nextflow_config - Config default value correct: params.normalisation_mode= Spikein
nextflow_config - Config default value correct: params.normalisation_binsize= 50
nextflow_config - Config default value correct: params.peakcaller= seacr
nextflow_config - Config default value correct: params.use_control= true
nextflow_config - Config default value correct: params.extend_fragments= true
nextflow_config - Config default value correct: params.igg_scale_factor= 0.5
nextflow_config - Config default value correct: params.seacr_peak_threshold= 0.05
nextflow_config - Config default value correct: params.seacr_norm= non
nextflow_config - Config default value correct: params.seacr_stringent= stringent
nextflow_config - Config default value correct: params.macs2_qvalue= 0.01
nextflow_config - Config default value correct: params.macs_gsize= 2700000000.0
nextflow_config - Config default value correct: params.macs2_narrow_peak= true
nextflow_config - Config default value correct: params.macs2_broad_cutoff= 0.1
nextflow_config - Config default value correct: params.consensus_peak_mode= group
nextflow_config - Config default value correct: params.replicate_threshold= 1.0
nextflow_config - Config default value correct: params.igv_show_gene_names= true
nextflow_config - Config default value correct: params.dt_qc_bam_binsize= 500
nextflow_config - Config default value correct: params.dt_qc_corr_method= pearson
nextflow_config - Config default value correct: params.dt_heatmap_gene_beforelen= 3000
nextflow_config - Config default value correct: params.dt_heatmap_gene_bodylen= 5000
nextflow_config - Config default value correct: params.dt_heatmap_gene_afterlen= 3000
nextflow_config - Config default value correct: params.dt_heatmap_peak_beforelen= 3000
nextflow_config - Config default value correct: params.dt_heatmap_peak_afterlen= 3000
nextflow_config - Config default value correct: params.dt_calc_all_matrix= true
nextflow_config - Config default value correct: params.min_frip_overlap= 0.2
nextflow_config - Config default value correct: params.min_peak_overlap= 0.2
nextflow_config - Config default value correct: params.igv_sort_by_groups= true
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
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/CONTRIBUTING.md 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 - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-cutandrun_logo_light.png matches the template
files_unchanged - docs/images/nf-core-cutandrun_logo_light.png matches the template
files_unchanged - docs/images/nf-core-cutandrun_logo_dark.png matches the template
files_unchanged - docs/README.md 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: 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 (290 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: linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awstest.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 2.12.1
Run at 2024-02-01 11:42:12

chris-cheshire added 27 commits November 7, 2023 13:28

Update version

1847de9

Run multiqc when running some only keywords

ae11418

Improve igg ctrl matching with target samples

054e040

Update version

ad99e9f

Add option to change sample grouping in igv output

bb59ea5

Add ability to dump scale factor values out of the pipeline

1cea405

Update scale factor dump

55dac76

Update logging

1575fd0

Auto scale igv groups together

81baaf1

Group samples on group in igv

448b192

Update metadata

f0a800a

Update igg control mapping

d4fa90d

black updating

6970c85

Update for tech reps

a6bdc2c

Merge remote-tracking branch 'nf-core/nf-core-template-merge-2.12' in…

19ebcc5

…to template-merge

Update schema

cbf9cf8

Prettier formating

7e779ef

Update template

0d50fff

Update schema

f518d1e

Update local versions

80a3e69

Update schema

4238a79

Update versions

3bdd809

Update changelog

da78f72

Merge branch 'template-merge' into dev

957b7ab

Whitespace

037a62b

whitespace

4407282

Merge pull request #217 from luslab/dev

f1b7994

Updates

tamara-hodgetts approved these changes Feb 1, 2024

View reviewed changes

amchakra self-requested a review February 1, 2024 15:27

amchakra approved these changes Feb 1, 2024

View reviewed changes

chris-cheshire merged commit 6e1125d into master Feb 1, 2024

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3.2.2 Release Candidiate #230

3.2.2 Release Candidiate #230

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chris-cheshire commented Feb 1, 2024

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3.2.2 Release Candidiate #230

3.2.2 Release Candidiate #230

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chris-cheshire commented Feb 1, 2024

[3.2.2] - 2024-02-01

Enhancements

Fixes

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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github-actions bot commented Feb 1, 2024 •

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