Publish peripheral data as well, even if we don't use it ourselves

muffato commented 1 month ago

TOLIT-2200

This PR is to publish more output files from the pipeline. Those things were not originally included because we don't need them ourselves (we'll get the files via other pipelines) but someone running the pipeline may find those interesting.

At the same time, I found that the full-test didn't pass because of some recent changes I did.

Keeping it as a draft for now until the base branch is merged. I also need to document the changes in docs/output.md

PR checklist

[ ] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[ ] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).

github-actions[bot] commented 1 month ago

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

Posted for pipeline commit aef0532

+| ✅ 133 tests passed       |+
#| ❔  24 tests were ignored |#
!| ❗   1 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config ``manifest.version`` should end in ``dev``: ``0.5.0`` ### :grey_question: Tests ignored: * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File is ignored: `CODE_OF_CONDUCT.md` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File is ignored: `assets/nf-core-blobtoolkit_logo_light.png` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-blobtoolkit_logo_light.png` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-blobtoolkit_logo_dark.png` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File is ignored: `.github/ISSUE_TEMPLATE/config.yml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File is ignored: `.github/workflows/awstest.yml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File is ignored: `.github/workflows/awsfulltest.yml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File is ignored: `conf/igenomes.config` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable ignored: `manifest.name` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable ignored: `manifest.homePage` * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - File ignored due to lint config: `CODE_OF_CONDUCT.md` * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - File ignored due to lint config: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md` * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/ISSUE_TEMPLATE/bug_report.yml` * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - File does not exist: `.github/ISSUE_TEMPLATE/config.yml` * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/PULL_REQUEST_TEMPLATE.md` * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/workflows/branch.yml` * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/workflows/linting.yml` * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - File ignored due to lint config: `assets/nf-core-blobtoolkit_logo_light.png` * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - File ignored due to lint config: `docs/images/nf-core-blobtoolkit_logo_light.png` * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - File ignored due to lint config: `docs/images/nf-core-blobtoolkit_logo_dark.png` * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - File ignored due to lint config: `lib/NfcoreTemplate.groovy` * [actions_awstest](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/actions_awstest.html) - 'awstest.yml' workflow not found: `/home/runner/work/blobtoolkit/blobtoolkit/.github/workflows/awstest.yml` * [template_strings](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/template_strings.html) - template_strings * [merge_markers](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/merge_markers.html) - merge_markers ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `.gitattributes` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `.gitignore` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `.nf-core.yml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `.editorconfig` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `.prettierignore` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `.prettierrc.yml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `CHANGELOG.md` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `CITATIONS.md` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `nextflow_schema.json` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `nextflow.config` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `README.md` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `.github/.dockstore.yml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `.github/CONTRIBUTING.md` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/bug_report.yml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/feature_request.yml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `.github/PULL_REQUEST_TEMPLATE.md` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `.github/workflows/branch.yml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `.github/workflows/ci.yml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `.github/workflows/linting_comment.yml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `.github/workflows/linting.yml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `assets/email_template.html` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `assets/email_template.txt` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `assets/sendmail_template.txt` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `conf/modules.config` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `conf/test.config` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `conf/test_full.config` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `docs/output.md` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `docs/usage.md` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `lib/nfcore_external_java_deps.jar` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `lib/NfcoreTemplate.groovy` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `lib/Utils.groovy` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `lib/WorkflowMain.groovy` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `main.nf` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `assets/multiqc_config.yml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `conf/base.config` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `lib/WorkflowBlobtoolkit.groovy` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `modules.json` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File found: `pyproject.toml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File not found check: `Singularity` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File not found check: `parameters.settings.json` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File not found check: `pipeline_template.yml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File not found check: `.nf-core.yaml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File not found check: `bin/markdown_to_html.r` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File not found check: `conf/aws.config` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File not found check: `.github/workflows/push_dockerhub.yml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File not found check: `.github/ISSUE_TEMPLATE/bug_report.md` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File not found check: `.github/ISSUE_TEMPLATE/feature_request.md` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File not found check: `docs/images/nf-core-blobtoolkit_logo.png` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File not found check: `.markdownlint.yml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File not found check: `.yamllint.yml` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File not found check: `lib/Checks.groovy` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File not found check: `lib/Completion.groovy` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File not found check: `lib/Workflow.groovy` * [files_exist](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_exist.html) - File not found check: `.travis.yml` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `manifest.nextflowVersion` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `manifest.description` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `manifest.version` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `timeline.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `trace.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `report.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `dag.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `process.cpus` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `process.memory` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `process.time` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `params.outdir` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `params.input` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `params.validationShowHiddenParams` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `params.validationSchemaIgnoreParams` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `manifest.mainScript` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `timeline.file` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `trace.file` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `report.file` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable found: `dag.file` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.nf_required_version` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.container` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.singleEnd` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.igenomesIgnore` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.name` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.enable_conda` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config ``timeline.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config ``report.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config ``trace.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config ``dag.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config ``dag.file`` ended with ``.html`` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config variable ``manifest.nextflowVersion`` started with >= or !>= * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - Config `params.custom_config_version` is set to `master` * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_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/2.11/pipeline_lint_tests/nextflow_config.html) - Lines for loading custom profiles found * [nextflow_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/nextflow_config.html) - nextflow.config contains configuration profile `test` * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - `.gitattributes` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - `.prettierrc.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - `.github/.dockstore.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - `.github/CONTRIBUTING.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - `.github/ISSUE_TEMPLATE/feature_request.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - `.github/workflows/linting_comment.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - `assets/email_template.html` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - `assets/email_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - `assets/sendmail_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - `docs/README.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - `lib/nfcore_external_java_deps.jar` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - `.gitignore` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - `.prettierignore` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/files_unchanged.html) - `pyproject.toml` matches the template * [actions_ci](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/actions_ci.html) - '.github/workflows/ci.yml' is triggered on expected events * [actions_ci](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/actions_ci.html) - '.github/workflows/ci.yml' checks minimum NF version * [readme](https://nf-co.re/tools/docs/2.11/pipeline_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/2.11/pipeline_lint_tests/readme.html) - README Zenodo placeholder was replaced with DOI. * [pipeline_todos](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/pipeline_todos.html) - No TODO strings found * [pipeline_name_conventions](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/pipeline_name_conventions.html) - Name adheres to nf-core convention * [schema_lint](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/schema_lint.html) - Schema lint passed * [schema_lint](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/schema_lint.html) - Schema title + description lint passed * [schema_lint](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/schema_lint.html) - Input mimetype lint passed: 'text/csv' * [schema_params](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/schema_params.html) - Schema matched params returned from nextflow config * [system_exit](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/system_exit.html) - No `System.exit` calls found * [actions_schema_validation](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: fix-linting.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: sanger_test.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: branch.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: linting_comment.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: linting.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: clean-up.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: sanger_test_full.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: release-announcements.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: ci.yml * [modules_json](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/modules_json.html) - Only installed modules found in `modules.json` * [multiqc_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains `report_section_order` * [multiqc_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains `export_plots` * [multiqc_config](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains `report_comment` * [multiqc_config](https://nf-co.re/tools/docs/2.11/pipeline_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/2.11/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains 'export_plots: true'. * [modules_structure](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/modules_structure.html) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL' ### Run details * nf-core/tools version 2.11 * Run at `2024-07-01 16:13:42`

muffato commented 4 weeks ago

It's ready for review

gq1 commented 4 weeks ago

I can see master still being used in this ci? https://github.com/sanger-tol/blobtoolkit/blob/dev/.github/workflows/branch.yml

if you haven't changed anywhere else, I can do a quick PR.

muffato commented 4 weeks ago

I can see master still being used in this ci? https://github.com/sanger-tol/blobtoolkit/blob/dev/.github/workflows/branch.yml

if you haven't changed anywhere else, I can do a quick PR.

Yes, please

gq1 commented 4 weeks ago

I have successfully run both test and test_raw profile on the farm as a new users.

Except the error with the two newly pulled singularity images: docker.io-pacificbiosciences-pyyaml-5.3.1.img docker.io-genomehubs-blobtk-0.5.1.img

And the error message:

Command error:
  FATAL:   container creation failed: mount /proc/self/fd/12->/software/singularity/3.11.4/var/singularity/mnt/session/rootfs error: while mounting image /proc/self/fd/12: kernel reported a bad superblock for squashfs image partition, possible causes are that your kernel doesn't support the compression algorithm or the image is corrupted

I have tried different version of singualrity on the new farm, all have the same problem. This is probably caused by a combination of farm22 and docker image?

muffato commented 3 days ago

Since #97 is taking a while, I've rebased this branch onto dev

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sanger-tol / blobtoolkit