v0.3 - Pipeline now validated on five real genomes

muffato commented 5 months ago

I've now tested the pipeline on five real, complete, genomes (though all under 100 Mbp). This PR is to fix all the issues I've found along the way:

Fixed the conditional runs of blastn
Fixed the generation of the no-hit list
Fixed the conversion of the unaligned input files to Fasta
Fixed the documentation about preparing the NT database
Fixed the detection of the NT database in the nf-core module
The pipeline now supports samplesheets generated by the nf-core/fetchngs pipeline by passing the --fetchngs_samplesheet true option.
FastQ files can bypass the conversion to Fasta
Fixed missing BUSCO results from the blobdir (only 1 BUSCO was loaded)
Fixed the default category used to colour the blob plots

I want to release this as the version 0.3. The following is still needed for the version 1.0:

Validation on >100 Mbp genomes, possibly with some improved resource requests.
Validation on the usage for non public assemblies.

which may require another 0.* release.

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 5 months ago

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

Posted for pipeline commit ff87d76

+| ✅ 134 tests passed       |+
#| ❔  23 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``: ``0.2.0`` ### :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) - 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`.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/branch.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: 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: linting_comment.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: ci.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: clean-up.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: 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: fix-linting.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 `2024-02-09 11:28:25`

github-actions[bot] commented 5 months 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:

Install black: pip install black
Fix formatting errors in your pipeline: black .

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

We highly recommend setting up Black 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!

muffato commented 5 months ago

Ignore the prettier error for now. .devcontainer/devcontainer.json hasn't changed since the last pull-request, where it passed prettier. The CI must be picking up a new version of prettier which we don't have on the farm yet. Will be addressed later.

muffato commented 5 months ago

To run on the farm, use these arguments:

--taxdump /lustre/scratch123/tol/resources/taxonomy/latest/new_taxdump
--busco /lustre/scratch123/tol/resources/busco/latest
--blastp /lustre/scratch123/tol/resources/uniprot_reference_proteomes/latest/reference_proteomes.dmnd
--blastx /lustre/scratch123/tol/resources/uniprot_reference_proteomes/latest/reference_proteomes.dmnd
--blastn /lustre/scratch123/tol/teams/tolit/users/mm49/nextflow/btk/prod_test/new_nt/untar

(there isn't a central NT database with taxonomy information yet. It's still in progress)

muffato commented 5 months ago

Prettier error fixed, thanks to @BethYates

BethYates commented 4 months ago

The code looks good but the images aren't being published to the results directory

muffato commented 4 months ago

@BethYates

The images are now published in their directory
Introduced an output directory named blobtoolkit and turned BUSCO to lower case.
Images as PNG by default, but SVG can be generated with the option --image_format svg
I had to pin the version of nf-core for the linting to pass

sanger-tol / blobtoolkit