Deprecate module parameter #148

nictru · 2024-06-14T10:45:06Z

This PR removes the module parameter from the pipeline. It was used for selecting which sections of the pipeline should be executed. It had the following allowed values:

circrna_discovery: This was redundant because the pipeline could not be executed without it
differential_expression: This section has been entirely removed via Clean up differential expression workflow #147
mirna_prediction: This is the only section where disabling makes sense. However, this can also be toggled via the mature parameter. If it is not provided, the mirna_prediction processes will not be executed. So the module parameter also doesn't offer any benefit here.

So the parameter is entirely redundant and removed via this PR.

github-actions · 2024-06-14T10:46:51Z

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

Posted for pipeline commit ab74eb5

+| ✅ 217 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).

✅ 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
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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: 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-circrna_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-circrna_logo_light.png
files_exist - File found: docs/images/nf-core-circrna_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-circrna_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/WorkflowCircrna.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: 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: dev
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.tool= circexplorer2
nextflow_config - Config default value correct: params.bsj_reads= 0
nextflow_config - Config default value correct: params.tool_filter= 0
nextflow_config - Config default value correct: params.duplicates_fun= mean
nextflow_config - Config default value correct: params.save_intermediates= false
nextflow_config - Config default value correct: params.exon_boundary= 200
nextflow_config - Config default value correct: params.sjdboverhang= 100
nextflow_config - Config default value correct: params.chimJunctionOverhangMin= 10
nextflow_config - Config default value correct: params.alignSJDBoverhangMin= 10
nextflow_config - Config default value correct: params.limitSjdbInsertNsj= 1000000
nextflow_config - Config default value correct: params.chimSegmentMin= 10
nextflow_config - Config default value correct: params.seglen= 25
nextflow_config - Config default value correct: params.min_intron= 20
nextflow_config - Config default value correct: params.max_intron= 1000000
nextflow_config - Config default value correct: params.min_map_len= 40
nextflow_config - Config default value correct: params.min_fusion_distance= 200
nextflow_config - Config default value correct: params.bootstrap_samples= 30
nextflow_config - Config default value correct: params.save_unaligned= false
nextflow_config - Config default value correct: params.save_reference= true
nextflow_config - Config default value correct: params.hisat2_build_memory= 200.GB
nextflow_config - Config default value correct: params.skip_trimming= false
nextflow_config - Config default value correct: params.save_trimmed= false
nextflow_config - Config default value correct: params.skip_fastqc= false
nextflow_config - Config default value correct: params.min_trimmed_reads= 10000
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= 50
nextflow_config - Config default value correct: params.max_memory= 300.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/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-circrna_logo_light.png matches the template
files_unchanged - docs/images/nf-core-circrna_logo_light.png matches the template
files_unchanged - docs/images/nf-core-circrna_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
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (379 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: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 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'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
modules_config - CLEAN_FASTA found in conf/modules.config and Nextflow scripts.
modules_config - SEQKIT_SPLIT found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE_BUILD found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE2_BUILD found in conf/modules.config and Nextflow scripts.
modules_config - BWA_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - HISAT2_EXTRACTSPLICESITES found in conf/modules.config and Nextflow scripts.
modules_config - HISAT2_BUILD found in conf/modules.config and Nextflow scripts.
modules_config - STAR_GENOMEGENERATE found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_BSJS found in conf/modules.config and Nextflow scripts.
modules_config - ANNOTATION found in conf/modules.config and Nextflow scripts.
modules_config - UPSET_SAMPLES found in conf/modules.config and Nextflow scripts.
modules_config - UPSET_ALL found in conf/modules.config and Nextflow scripts.
modules_config - ADD_BACKSPLICE found in conf/modules.config and Nextflow scripts.
modules_config - COMBINE_TRANSCRIPTOME_GTFS found in conf/modules.config and Nextflow scripts.
modules_config - EXCLUDE_OVERLONG_TRANSCRIPTS found in conf/modules.config and Nextflow scripts.
modules_config - MARK_CIRCULAR found in conf/modules.config and Nextflow scripts.
modules_config - TARGETSCAN_DATABASE found in conf/modules.config and Nextflow scripts.
modules_config - TARGETSCAN found in conf/modules.config and Nextflow scripts.
modules_config - MIRANDA found in conf/modules.config and Nextflow scripts.
modules_config - MIRNA_TARGETS 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 2024-06-14 13:07:07

conf/modules.config

Diana Bassow added 2 commits June 14, 2024 12:38

Change conditions for downstream tasks

aac8f81

Changed documentation 'phenotype' and 'mature'

d24d1ba

nictru linked an issue Jun 14, 2024 that may be closed by this pull request

Deprecate the module parameter #145

Closed

nictru added 10 commits June 14, 2024 12:53

Remove module traces of module parameter

c046322

Fix nextflow_schema.json

d7b6258

Make phenotype optional for quantification

d73a8c2

Improve documentation of the phenotype parameter

fdc9667

Update documentation for enabling miRNA prediction

9f9e967

Update README

a0fb084

Update usage documentation to follow rnaseq example

7fb28ad

Update nextflow schema order

1d66688

Update ouput docs

ee159a2

Prettier

ab74eb5

mahesh-panchal approved these changes Jun 14, 2024

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nictru merged commit c7077d9 into dev Jun 15, 2024
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nictru deleted the deprecate_module branch June 15, 2024 06:40

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Deprecate module parameter #148

Deprecate module parameter #148

nictru commented Jun 14, 2024

github-actions bot commented Jun 14, 2024 •

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Deprecate module parameter #148

Deprecate module parameter #148

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nictru commented Jun 14, 2024

github-actions bot commented Jun 14, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

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✅ Tests passed:

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github-actions bot commented Jun 14, 2024 •

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