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🚨 solve linter issues related to VScode and nextflow languageserver #87

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🚨 solve linter issues related to VScode and nextflow languageserver #87

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@bunop bunop commented Jan 20, 2025 •
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bunop added 12 commits January 20, 2025 11:32
@bunop
🚚 move REMOVE_OVERLAP into CRAM_FREEBAYES_PARALLEL workflow
296ea86
@bunop
✨ start pipeline_initialization subworkflow
336a8fd 
start moving stuff in a dedicated workflow
@bunop
🎨 set custom indentation in editorconfig
bb333e4
@bunop
🚚 move stuff in workflow
4150829
@bunop
⬆️ update MultiQC module
df1e1fa
@bunop
⬆️ update snpeff/download
996f065
@bunop
🔧 update .editorconfig
13005f6
@bunop
⬆️ update snpeff/snpeff
be05526
@bunop
🔥 remove REMOVE_OVERLAP
e150eb2 
remove a passage with bcftools/norm: there are no difference between bcftools/concat -Da (FREEBAYES_CONCAT)
@bunop
🔧 refactor modules.config
e5d09cb 
fix errors and simplify structure
@bunop
🔧 pin snpeff/download and snpeff/snpeff
d56e5a3 
pinning snpeff from updates in order to avoid issues with patches
@bunop
⬆️ update modules
79fab26 
general module update
@bunop bunop added enhancement New feature or request performance Improve the performance or better resource management labels Jan 20, 2025
@bunop bunop added this to the release v0.6.2 milestone Jan 20, 2025
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github-actions bot commented Jan 20, 2025 •
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nf-core pipelines lint overall result: Passed ✅

Posted for pipeline commit f12b6a2

+| ✅ 101 tests passed       |+
#| ❔  48 tests were ignored |#

❔ 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

✅ 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: linting_comment.yml
  • actions_schema_validation - Workflow validation passed: linting.yml
  • actions_schema_validation - Workflow validation passed: download_pipeline.yml
  • actions_schema_validation - Workflow validation passed: fix-linting.yml
  • actions_schema_validation - Workflow validation passed: branch.yml
  • actions_schema_validation - Workflow validation passed: template_version_comment.yml
  • actions_schema_validation - Workflow validation passed: ci.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 - FREEBAYES_CONCAT found in conf/modules.config and Nextflow scripts.
  • modules_config - FREEBAYES_CONCAT_TABIX found in conf/modules.config and Nextflow scripts.
  • modules_config - FREEBAYES_NORM 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_FILLTAGS found in conf/modules.config and Nextflow scripts.
  • modules_config - BCFTOOLS_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: 3.1.2

Run details

  • nf-core/tools version 3.1.2
  • Run at 2025-01-22 13:33:48

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enhancement New feature or request performance Improve the performance or better resource management
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release v0.6.2
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