:bookmark: pipeline release v0.3.0

bunop commented 2 years ago

This release let pipeline be managed with latest nf-core/tools. Configurations changed in order to be executed even in AWS environment. Issue #10 is partially completed by activating CI and configuring pipelines like the nf-core templates

closes #2
closes #7

github-actions[bot] commented 2 years ago

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

Posted for pipeline commit 852ce50

+| ✅  12 tests passed       |+
#| ❔  27 tests were ignored |#
!| ❗  34 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README did not have a Nextflow minimum version badge. * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README did not have a Nextflow minimum version mentioned in Quick Start section. * [pipeline_name_conventions](https://nf-co.re/tools-docs/lint_tests/pipeline_name_conventions.html) - Naming does not adhere to nf-core conventions: Contains non alphanumeric characters * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `reads_path` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `genome_path` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `clip_r1` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `clip_r2` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `three_prime_clip_r1` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `three_prime_clip_r2` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `multiqc_config` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `multiqc_title` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `max_multiqc_email_size` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `trim_nextseq` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `save_trimmed` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `skip_trimming` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `tracedir` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `email` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `email_on_fail` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `plaintext_email` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `monochrome_logs` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `help` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `validate_params` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `show_hidden_params` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `singularity_pull_docker_container` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `custom_config_version` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `custom_config_base` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `hostnames` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `config_profile_description` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `config_profile_contact` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `config_profile_url` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `config_profile_name` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `max_memory` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `max_cpus` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `max_time` ### :grey_question: Tests ignored: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - files_exist * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - nextflow_config * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `CODE_OF_CONDUCT.md` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `.github/.dockstore.yml` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `.github/CONTRIBUTING.md` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `.github/ISSUE_TEMPLATE/bug_report.md` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `.github/ISSUE_TEMPLATE/config.yml` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `.github/ISSUE_TEMPLATE/feature_request.md` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `.github/PULL_REQUEST_TEMPLATE.md` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `.github/workflows/branch.yml` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/workflows/linting.yml` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `assets/email_template.html` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `assets/email_template.txt` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `assets/sendmail_template.txt` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `assets/nf-core-cnr-ibba/nf-resequencing-mem_logo.png` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `docs/images/nf-core-cnr-ibba/nf-resequencing-mem_logo.png` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `docs/README.md` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `lib/nfcore_external_java_deps.jar` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `lib/NfcoreSchema.groovy` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `lib/NfcoreTemplate.groovy` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.gitignore` or `foo` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `assets/multiqc_config.yaml` * [actions_ci](https://nf-co.re/tools-docs/lint_tests/actions_ci.html) - actions_ci * [actions_awstest](https://nf-co.re/tools-docs/lint_tests/actions_awstest.html) - 'awstest.yml' workflow not found: `/home/runner/work/nf-resequencing-mem/nf-resequencing-mem/.github/workflows/awstest.yml` * [actions_awsfulltest](https://nf-co.re/tools-docs/lint_tests/actions_awsfulltest.html) - actions_awsfulltest * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - pipeline_todos * [merge_markers](https://nf-co.re/tools-docs/lint_tests/merge_markers.html) - merge_markers ### :white_check_mark: Tests passed: * [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) - `.markdownlint.yml` 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/workflows/linting_comment.yml` matches the template * [template_strings](https://nf-co.re/tools-docs/lint_tests/template_strings.html) - Did not find any Jinja template strings (58 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: ci.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: linting_comment.yml * [modules_json](https://nf-co.re/tools-docs/lint_tests/modules_json.html) - Only installed modules found in `modules.json` ### Run details * nf-core/tools version 2.2.dev0 * Run at `2021-11-08 15:28:06`

github-actions[bot] commented 2 years ago

Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks. To fix this CI test, please run:

Install markdownlint-cli
- On Mac: brew install markdownlint-cli
- Everything else: Install npm then install markdownlint-cli (npm install -g markdownlint-cli)
Fix the markdown errors
- Automatically: markdownlint . --fix
- Manually resolve anything left from markdownlint .

Once you push these changes the test should pass, and you can hide this comment :+1:

We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

github-actions[bot] commented 2 years ago

YAML linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks. To fix this CI test, please run:

Install yaml-lint
- Install npm then install yaml-lint (npm install -g yaml-lint)
Fix the markdown errors
- Run the test locally: yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")
- Fix any reported errors in your YAML files

Once you push these changes the test should pass, and you can hide this comment :+1:

We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

cnr-ibba / nf-resequencing-mem