🔖 release v0.6.2

[bunop]

• Add a parameter to skip normalization subworkflow (closes 🔧 configure options and conditional steps #90)
• Update freebayes to version 1.3.8 (closes ⬆️ upgrade freebayes to the latest release #88)
• Solve linter issues related to VScode and nextflow languageserver plugin (closes 🚨 solve linter issues related to VScode and nextflow languageserver #86)
• Update .editorconfig
• Update modules
• Restructure modules.config
• Move functions inside workflows
• Convert freebayes specific parameters in pipeline parameters (closes ✨ convert freebayes specific parameters in pipeline parameters #80)
• Update nextflow.config
• Support for institutional configuration
• Parallelize normalization steps by chromosomes. Merge VCF files after normalization
• Normalize VCF file using vcfwave (closes 💥 normalize VCF files #76 )
• Add normalize_vcf local subworkflow
• Update nextflow to version 24.04.0
• Using the resourceLimits directive to set the max requirements for each process
• update CI system (closes 👷 update CI system #81)
• Use remote files when testing pipeline
• Fixed issue with picard/markduplicates (closes 🐛 markduplicates has issues with cram files #77)
• Display current chromosome in samtools/depth

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 02e6160

+| ✅ 104 tests passed       |+
#| ❔  49 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

• local_component_structure - samplesheet_check.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - vcflib_vcfwave.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - bcftools_filltags.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - freebayes_splitcram.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - pipeline_initialization.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - snpeff_annotate.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - freebayes_normalize.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - prepare_genome.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: conf/igenomes_ignored.config
• files_exist - File is ignored: CODE_OF_CONDUCT.md
• files_exist - File is ignored: assets/nf-core-nf-resequencing-mem_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-nf-resequencing-mem_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-nf-resequencing-mem_logo_dark.png
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• files_exist - File is ignored: ro-crate-metadata.json
• files_exist - File is ignored: .github/.dockstore.yml
• files_exist - File is ignored: .github/CONTRIBUTING.md
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/bug_report.yml
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/feature_request.yml
• files_exist - File is ignored: .github/PULL_REQUEST_TEMPLATE.md
• files_exist - File is ignored: assets/email_template.html
• files_exist - File is ignored: assets/email_template.txt
• files_exist - File is ignored: assets/sendmail_template.txt
• files_exist - File is ignored: conf/test_full.config
• files_exist - File is ignored: docs/output.md
• files_exist - File is ignored: docs/README.md
• files_exist - File is ignored: docs/README.md
• files_exist - File is ignored: docs/usage.md
• files_exist - File is ignored: .markdownlint.yml
• files_exist - File is ignored: lib/NfcoreTemplate.groovy
• files_exist - File is ignored: lib/Utils.groovy
• files_exist - File is ignored: lib/WorkflowMain.groovy
• files_exist - File is ignored: lib/nfcore_external_java_deps.jar
• nextflow_config - nextflow_config
• files_unchanged - File does not exist: CODE_OF_CONDUCT.md
• files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_unchanged - File does not exist: .github/.dockstore.yml
• files_unchanged - File does not exist: .github/CONTRIBUTING.md
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/bug_report.yml
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/feature_request.yml
• files_unchanged - File does not exist: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File does not exist: assets/email_template.html
• files_unchanged - File does not exist: assets/email_template.txt
• files_unchanged - File does not exist: assets/sendmail_template.txt
• files_unchanged - File does not exist: assets/nf-core-nf-resequencing-mem_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-nf-resequencing-mem_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-nf-resequencing-mem_logo_dark.png
• files_unchanged - File does not exist: docs/README.md
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/nf-resequencing-mem/nf-resequencing-mem/.github/workflows/awstest.yml
• pipeline_todos - pipeline_todos
• pipeline_name_conventions - pipeline_name_conventions
• included_configs - included_configs

✅ 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: 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/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: conf/modules.config
• files_exist - File found: conf/test.config
• 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: 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: .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-nf-resequencing-mem_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/Workflow.groovy
• files_exist - File not found check: lib/WorkflowNf-resequencing-mem.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: .travis.yml
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.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
• actions_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - '.github/workflows/ci.yml' checks minimum NF version
• readme - README Nextflow minimum version badge matched config. Badge: 24.04.0, Config: 24.04.0
• readme - README Zenodo placeholder was replaced with DOI.
• plugin_includes - No wrong validation plugin imports have been found
• 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: branch.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: template_version_comment.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: fix-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 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 'export_plots: true'.
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• base_config - FREEBAYES_CHUNK found in conf/base.config and Nextflow scripts.
• base_config - PICARD_MARKDUPLICATES found in conf/base.config and Nextflow scripts.
• base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - TABIX_BGZIP found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
• modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - SEQKIT_RMDUP_R1 found in conf/modules.config and Nextflow scripts.
• modules_config - SEQKIT_RMDUP_R2 found in conf/modules.config and Nextflow scripts.
• modules_config - TRIMGALORE found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
• modules_config - PICARD_MARKDUPLICATES found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_COVERAGE found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_DEPTH found in conf/modules.config and Nextflow scripts.
• modules_config - FREEBAYES_SPLITCRAM found in conf/modules.config and Nextflow scripts.
• modules_config - FREEBAYES_CHUNK found in conf/modules.config and Nextflow scripts.
• modules_config - CONCATENATE_CHROMS found in conf/modules.config and Nextflow scripts.
• modules_config - CONCATENATE_CHROMS_TABIX found in conf/modules.config and Nextflow scripts.
• modules_config - FREEBAYES_CONCAT found in conf/modules.config and Nextflow scripts.
• modules_config - VCFLIB_VCFWAVE found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_SORT found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_NORM found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_NORM_TABIX found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_FILLTAGS found in conf/modules.config and Nextflow scripts.
• modules_config - NORMALIZED_CONCAT found in conf/modules.config and Nextflow scripts.
• modules_config - SNPEFF_DOWNLOAD found in conf/modules.config and Nextflow scripts.
• modules_config - CUSTOM_DUMPSOFTWAREVERSIONS 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: 3.2.0
• version_consistency - Version tags are numeric and consistent between container, release tag and config.

Run details

• nf-core/tools version 3.2.0
• Run at 2025-02-05 13:08:28