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cnr-ibba / nf-resequencing-mem

Nextflow resequencing pipeline with bwa-mem and freebayes
MIT License
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:boom: install modules with latest nf-core #35

Closed bunop closed 1 year ago

bunop commented 1 year ago

Upgrading modules and fix issues after update

github-actions[bot] commented 1 year ago

Python linting (black) is failing

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

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github-actions[bot] commented 1 year ago

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

Posted for pipeline commit c988b39

+| ✅  13 tests passed       |+
#| ❔  28 tests were ignored |#
!| ❗  41 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_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Parameter `input` is not defined in the correct subschema (input_output_options) * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `input` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `genome_fasta` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `genome_fasta_fai` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `genome_bwa_index` * [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: `multiqc_logo` * [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: `save_bam` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `save_fasta_index` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - Ungrouped param in schema: `save_bwa_index` * [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.yml` * [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.yml` * [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-nf-resequencing-mem_logo_light.png` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `docs/images/nf-core-nf-resequencing-mem_logo_light.png` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `docs/images/nf-core-nf-resequencing-mem_logo_dark.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 `.prettierignore` or `pyproject.toml` * [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 * [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - multiqc_config ### :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) - `.prettierrc.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 (66 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` * [modules_structure](https://nf-co.re/tools-docs/lint_tests/modules_structure.html) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL' ### Run details * nf-core/tools version 2.6 * Run at `2022-10-28 16:14:08`