uncomment including pipeline config

[mirpedrol]

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[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d95cefc

+| ✅ 240 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

• nextflow_config - Config manifest.version should end in dev: 2.3.0
• pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
• pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
• pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
• pipeline_todos - TODO string in base.config: Check the defaults for all processes
• 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

❔ Tests ignored:

• files_exist - File is ignored: conf/test.config
• files_exist - File is ignored: conf/test_full.config
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ 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: conf/igenomes_ignored.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-crisprseq_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/WorkflowCrisprseq.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 - Found nf-schema plugin
• 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: validation.help.enabled
• 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 found: validation.help.beforeText
• nextflow_config - Config variable found: validation.help.afterText
• nextflow_config - Config variable found: validation.help.command
• nextflow_config - Config variable found: validation.summary.beforeText
• nextflow_config - Config variable found: validation.summary.afterText
• 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 variable (correctly) not found: params.max_cpus
• nextflow_config - Config variable (correctly) not found: params.max_memory
• nextflow_config - Config variable (correctly) not found: params.max_time
• nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
• nextflow_config - Config variable (correctly) not found: params.validationLenientMode
• nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
• nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
• 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.umi_bin_size= 1
• nextflow_config - Config default value correct: params.medaka_model= https://github.com/nanoporetech/medaka/raw/master/medaka/data/r941_min_high_g303_model.hdf5
• 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.hit_selection_iteration_nb= 1000.0
• nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
• 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.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.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
• 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/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-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: 24.04.2, Config: 24.04.2
• readme - README Zenodo placeholder was replaced with DOI.
• plugin_includes - No wrong validation plugin imports have been found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (0 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: branch.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: template_version_comment.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: awsfulltest_screening.yml
• actions_schema_validation - Workflow validation passed: ci.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 - ORIENT_REFERENCE found in conf/modules.config and Nextflow scripts.
• modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
• modules_config - PEAR found in conf/modules.config and Nextflow scripts.
• modules_config - BAGEL2_BF found in conf/modules.config and Nextflow scripts.
• modules_config - BAGEL2_PR found in conf/modules.config and Nextflow scripts.
• modules_config - BAGEL2_FC found in conf/modules.config and Nextflow scripts.
• modules_config - DRUGZ found in conf/modules.config and Nextflow scripts.
• modules_config - BAGEL2_GRAPH found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - FIND_ADAPTERS found in conf/modules.config and Nextflow scripts.
• modules_config - MAGECK_COUNT found in conf/modules.config and Nextflow scripts.
• modules_config - MAGECK_MLE found in conf/modules.config and Nextflow scripts.
• modules_config - MAGECK_TEST found in conf/modules.config and Nextflow scripts.
• modules_config - MAGECK_GRAPHRRA found in conf/modules.config and Nextflow scripts.
• modules_config - MAGECK_FLUTEMLE found in conf/modules.config and Nextflow scripts.
• modules_config - HITSELECTION found in conf/modules.config and Nextflow scripts.
• modules_config - HITSELECTION_MLE found in conf/modules.config and Nextflow scripts.
• modules_config - HITSELECTION_BAGEL2 found in conf/modules.config and Nextflow scripts.
• modules_config - HITSELECTION_RRA found in conf/modules.config and Nextflow scripts.
• modules_config - VENNDIAGRAM found in conf/modules.config and Nextflow scripts.
• modules_config - MAGECK_MLE_DAY0 found in conf/modules.config and Nextflow scripts.
• modules_config - CRISPRCLEANR_NORMALIZE found in conf/modules.config and Nextflow scripts.
• modules_config - CUTADAPT found in conf/modules.config and Nextflow scripts.
• modules_config - CUTADAPT_FIVE_PRIME found in conf/modules.config and Nextflow scripts.
• modules_config - CUTADAPT_THREE_PRIME found in conf/modules.config and Nextflow scripts.
• modules_config - SEQTK_SEQ_MASK found in conf/modules.config and Nextflow scripts.
• modules_config - EXTRACT_UMIS found in conf/modules.config and Nextflow scripts.
• modules_config - VSEARCH_CLUSTER found in conf/modules.config and Nextflow scripts.
• modules_config - VSEARCH_SORT found in conf/modules.config and Nextflow scripts.
• modules_config - PREPROCESSING_SUMMARY found in conf/modules.config and Nextflow scripts.
• modules_config - MATRICESCREATION found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_ALIGN_UMI_1 found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_ALIGN_UMI_2 found in conf/modules.config and Nextflow scripts.
• modules_config - RACON_1 found in conf/modules.config and Nextflow scripts.
• modules_config - RACON_2 found in conf/modules.config and Nextflow scripts.
• modules_config - MEDAKA found in conf/modules.config and Nextflow scripts.
• modules_config - SEQTK_SEQ_FATOFQ found in conf/modules.config and Nextflow scripts.
• modules_config - CLUSTERING_SUMMARY found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_ALIGN_ORIGINAL found in conf/modules.config and Nextflow scripts.
• modules_config - ALIGNMENT_SUMMARY found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - TEMPLATE_REFERENCE found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_ALIGN_TEMPLATE found in conf/modules.config and Nextflow scripts.
• modules_config - CIGAR_PARSER found in conf/modules.config and Nextflow scripts.
• modules_config - CRISPRSEQ_PLOTTER found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC 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: 3.0.2

Run details

• nf-core/tools version 3.0.2
• Run at 2024-10-29 11:04:18