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nf-core / rnavar

gatk4 RNA variant calling pipeline
https://nf-co.re/rnavar
MIT License
37 stars 32 forks source link

Addressed the review comments #56

Closed praveenraj2018 closed 2 years ago

praveenraj2018 commented 2 years ago

Mostly addressed the review comments

PR checklist

github-actions[bot] commented 2 years ago

nf-core lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 1ea2855

+| ✅ 147 tests passed       |+
!| ❗   2 tests had warnings |!
### :heavy_exclamation_mark: Test warnings: * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``manifest.version`` should end in ``dev``: ``'1.0.0'`` * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README did not have a Nextflow minimum version badge. ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitattributes` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitignore` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.nf-core.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.editorconfig` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.prettierrc.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CHANGELOG.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CITATIONS.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CODE_OF_CONDUCT.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CODE_OF_CONDUCT.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `nextflow_schema.json` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `nextflow.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `README.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/.dockstore.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/CONTRIBUTING.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/bug_report.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/config.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/feature_request.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/PULL_REQUEST_TEMPLATE.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/branch.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/ci.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/linting_comment.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/linting.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/email_template.html` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/email_template.txt` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/sendmail_template.txt` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/nf-core-rnavar_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/modules.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/test.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/test_full.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/images/nf-core-rnavar_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/images/nf-core-rnavar_logo_dark.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/output.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/usage.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/nfcore_external_java_deps.jar` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/NfcoreSchema.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/NfcoreTemplate.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/Utils.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/WorkflowMain.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `main.nf` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/multiqc_config.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/base.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/igenomes.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/awstest.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/awsfulltest.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/WorkflowRnavar.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `modules.json` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `Singularity` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `parameters.settings.json` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.nf-core.yaml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `bin/markdown_to_html.r` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `conf/aws.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.github/workflows/push_dockerhub.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.github/ISSUE_TEMPLATE/bug_report.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.github/ISSUE_TEMPLATE/feature_request.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `docs/images/nf-core-rnavar_logo.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.markdownlint.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.yamllint.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.travis.yml` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.name` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.nextflowVersion` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.description` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.version` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.homePage` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `timeline.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `trace.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `report.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `dag.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.cpus` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.memory` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.time` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.outdir` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.input` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.show_hidden_params` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.schema_ignore_params` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.mainScript` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `timeline.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `trace.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `report.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `dag.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.version` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.nf_required_version` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.container` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.singleEnd` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.igenomesIgnore` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.name` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``timeline.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``report.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``trace.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``dag.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``manifest.name`` began with ``nf-core/`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable ``manifest.homePage`` began with https://github.com/nf-core/ * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``dag.file`` ended with ``.html`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable ``manifest.nextflowVersion`` started with >= or !>= * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config `params.custom_config_version` is set to `master` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config `params.custom_config_base` is set to `https://raw.githubusercontent.com/nf-core/configs/master` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Lines for loading custom profiles found * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.gitattributes` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.prettierrc.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `CODE_OF_CONDUCT.md` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `LICENSE` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/.dockstore.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/CONTRIBUTING.md` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/ISSUE_TEMPLATE/bug_report.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/ISSUE_TEMPLATE/config.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/ISSUE_TEMPLATE/feature_request.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/PULL_REQUEST_TEMPLATE.md` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/workflows/branch.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/workflows/linting_comment.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/workflows/linting.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/email_template.html` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/email_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/sendmail_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/nf-core-rnavar_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `docs/images/nf-core-rnavar_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `docs/images/nf-core-rnavar_logo_dark.png` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `docs/README.md` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `lib/nfcore_external_java_deps.jar` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `lib/NfcoreSchema.groovy` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `lib/NfcoreTemplate.groovy` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.gitignore` matches the template * [actions_ci](https://nf-co.re/tools-docs/lint_tests/actions_ci.html) - '.github/workflows/ci.yml' is triggered on expected events * [actions_ci](https://nf-co.re/tools-docs/lint_tests/actions_ci.html) - '.github/workflows/ci.yml' checks minimum NF version * [actions_awstest](https://nf-co.re/tools-docs/lint_tests/actions_awstest.html) - '.github/workflows/awstest.yml' is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools-docs/lint_tests/actions_awsfulltest.html) - `.github/workflows/awsfulltest.yml` is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools-docs/lint_tests/actions_awsfulltest.html) - `.github/workflows/awsfulltest.yml` does not use `-profile test` * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README Nextflow minimum version in Quick Start section matched config. README: `21.10.3`, Config: `21.10.3` * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - No TODO strings found * [pipeline_name_conventions](https://nf-co.re/tools-docs/lint_tests/pipeline_name_conventions.html) - Name adheres to nf-core convention * [template_strings](https://nf-co.re/tools-docs/lint_tests/template_strings.html) - Did not find any Jinja template strings (159 files) * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Schema lint passed * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Schema title + description lint passed * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Schema matched params returned from nextflow config * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: awstest.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: linting.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: awsfulltest.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: branch.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: fix-linting.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: linting_comment.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: ci.yml * [merge_markers](https://nf-co.re/tools-docs/lint_tests/merge_markers.html) - No merge markers found in pipeline files * [modules_json](https://nf-co.re/tools-docs/lint_tests/modules_json.html) - Only installed modules found in `modules.json` * [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins. * [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains a matching 'report_comment'. * [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains 'export_plots: true'. ### Run details * nf-core/tools version 2.4.1 * Run at `2022-06-15 14:36:32`