search

nf-core / viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples
https://nf-co.re/viralrecon
MIT License
111 stars 104 forks source link

Apply samtools fixmate after ivar trim #396

Open wutron opened 9 months ago

wutron commented 9 months ago

Apply samtools fixmate to fix template length after primer trimming. Not necessary for viralrecon per se but cleans up alignment if user wants to use other tools downstream, e.g. samtools ampliconstats. https://github.com/samtools/samtools/blob/007d83e8b63737d8a08060723a41eba4a1df3f7a/amplicon_stats.c#L583

PR checklist

github-actions[bot] commented 9 months ago

nf-core lint overall result: Failed :x:

Posted for pipeline commit 0663ed2

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   5 tests had warnings |!
-| ❌   3 tests failed       |-
### :x: Test failures: * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `CODE_OF_CONDUCT.md` does not match the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/CONTRIBUTING.md` does not match the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/workflows/linting.yml` does not match the template ### :heavy_exclamation_mark: Test warnings: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found: `assets/multiqc_config.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found: `conf/igenomes.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found: `lib/WorkflowViralrecon.groovy` * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `methods_description_template.yml`: _#Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline_ * [system_exit](https://nf-co.re/tools-docs/lint_tests/system_exit.html) - `System.exit` in nanopore.nf: _System.exit(1)_ [line 237] ### :grey_question: Tests ignored: * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `assets/email_template.html` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `assets/email_template.txt` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `lib/NfcoreTemplate.groovy` * [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' not found ### :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: `.prettierignore` * [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-viralrecon_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-viralrecon_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/images/nf-core-viralrecon_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/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: `conf/base.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: `modules.json` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `pyproject.toml` * [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: `pipeline_template.yml` * [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-viralrecon_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: `lib/Checks.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `lib/Completion.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `lib/Workflow.groovy` * [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.validationShowHiddenParams` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.validationSchemaIgnoreParams` * [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.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 variable (correctly) not found: `params.enable_conda` * [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 ``manifest.version`` ends in ``dev``: ``2.7.0dev`` * [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) - `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/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) - `assets/sendmail_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/nf-core-viralrecon_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `docs/images/nf-core-viralrecon_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `docs/images/nf-core-viralrecon_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) - `.gitignore` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.prettierignore` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `pyproject.toml` 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 badge matched config. Badge: `23.04.0`, Config: `23.04.0` * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README Zenodo placeholder was replaced with DOI. * [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 (272 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_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Input mimetype lint passed: 'text/csv' * [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: fix-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: linting.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: clean-up.yml * [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_comment.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` * [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 2.10 * Run at `2023-10-16 14:51:24`