DSL2: Add multi-reference mapping support

jfy133 commented 1 year ago

Adds ability to provide a TSV file listing multiple references and their correpsonding indicies etc.

PR checklist

[x] 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 - add to the software_versions process and a regex to scrape_software_versions.py
- [ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
- [ ] If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repository.
[ ] Make sure your code lints (nf-core lint .).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker).
[ ] 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).

jfy133 commented 1 year ago

Current to do:

Add test data and a profile of referencesheet.tsv
Run tests cycling through presence of each column

jfy133 commented 1 year ago

@nf-core-bot fix linting

TCLamnidis commented 1 year ago

Please rename mitchondrion to mitochondrion_name

jfy133 commented 1 year ago

I vote mitochondrion_header

jfy133 commented 1 year ago

Next time: Continue updating modules.conf so all output files after mappign include the reference name Then official samplesheet (see testing/) and then actual testing

github-actions[bot] commented 1 year ago

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

Posted for pipeline commit 3ee3d9a

+| ✅ 158 tests passed       |+
!| ❗  19 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README contains the placeholder `zenodo.XXXXXXX`. This should be replaced with the zenodo doi (after the first release). * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `README.md`: _Include a figure that guides the user through the major workflow steps. Many nf-core_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `README.md`: _Fill in short bullet-pointed list of the default steps in the pipeline_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `nextflow.config`: _Specify your pipeline's command line flags_ * [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 prefered methods description, e.g. add publication citation for this pipeline_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `WorkflowMain.groovy`: _Add Zenodo DOI for pipeline after first release_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `test_full.config`: _Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `test_full.config`: _Give any required params for the test so that command line flags are not needed_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `base.config`: _Check the defaults for all processes_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `base.config`: _Customise requirements for specific processes._ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `test_humanbam.config`: _Specify the paths to your test data on nf-core/test-datasets_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `test_humanbam.config`: _Give any required params for the test so that command line flags are not needed_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `test.config`: _Specify the paths to your test data on nf-core/test-datasets_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `test.config`: _Give any required params for the test so that command line flags are not needed_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `eager.nf`: _Add all file path parameters for the pipeline to the list below_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `usage.md`: _Add documentation about anything specific to running your pipeline. 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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``: ``'3.0.0dev'`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - 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`lib/NfcoreSchema.groovy` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `lib/NfcoreTemplate.groovy` 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: `22.10.1`, Config: `22.10.1` * [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 (174 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 * [system_exit](https://nf-co.re/tools-docs/lint_tests/system_exit.html) - No `System.exit` calls found * [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: linting_comment.yml * [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: awstest.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: 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 * [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` * [multiqc_config](https://nf-co.re/tools-docs/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/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains a matching 'report_comment'. * [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains 'export_plots: true'. * [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 2.8 * Run at `2023-05-26 08:10:35`

jfy133 commented 1 year ago

Whoops edited your comment not quoting :facepalm:

[ ] (optional) Add deduplication to be ran with test_multiref profile

That should run by default, no?

what's up with failing manual tests?

I wanted to test it failed correctly because they were incompatioble tc.

TCLamnidis commented 1 year ago

Whoops edited your comment not quoting 🤦

[ ] (optional) Add deduplication to be ran with test_multiref profile

That should run by default, no?

Is this test profile implemented in the tests yet?

what's up with failing manual tests?

I wanted to test it failed correctly because they were incompatioble tc.

There was one marked with a question mark, where it didnt seem like expectation was a failure

jfy133 commented 1 year ago

Tested reference sheets

reference_sheet_multiref_test.zip

jfy133 commented 1 year ago

@nf-core-bot fix linting

jfy133 commented 1 year ago

I've made all the changes @TCLamnidis , however you and @scarlhoff's stupid HapMap poop-gen files have now broken the tests again...

ERROR ~ Invalid method invocation `call` with arguments: [[id:Mammoth_MT_Krause], /nf-core/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta, /home/runner/work/eager/eager/work/68/315f26b95b0aea12ecbd65f4320b86/Mammoth_MT_Krause.fasta.fai, /home/runner/work/eager/eager/work/c8/12f5e1a6486962f43ad873f4bc788a/Mammoth_MT_Krause.dict, /home/runner/work/eager/eager/work/ae/affedff2a287be10a59906aad52ca4/bwa, null, null, /home/runner/work/eager/eager/assets/angsd_resources/HapMapChrX.gz] (java.util.LinkedList) on _closure20 type

Following my previous notes to myself , there is a .map{ definition somewhere, where the HapMap position of a channel element is not given a variable name. However for teh life of me I cannot find where on earht this HapMap file is added to the reference indices.... so you guys need to find that and fix it, as this has come from you :grimacing: . Otherwise wierdly using the multiref CSV file (Rather than straight fasta), passes teh tests.

scarlhoff commented 1 year ago

I've made all the changes @TCLamnidis , however you and @scarlhoff's stupid HapMap poop-gen files have now broken the tests again...
ERROR ~ Invalid method invocation `call` with arguments: [[id:Mammoth_MT_Krause], /nf-core/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta, /home/runner/work/eager/eager/work/68/315f26b95b0aea12ecbd65f4320b86/Mammoth_MT_Krause.fasta.fai, /home/runner/work/eager/eager/work/c8/12f5e1a6486962f43ad873f4bc788a/Mammoth_MT_Krause.dict, /home/runner/work/eager/eager/work/ae/affedff2a287be10a59906aad52ca4/bwa, null, null, /home/runner/work/eager/eager/assets/angsd_resources/HapMapChrX.gz] (java.util.LinkedList) on _closure20 type
Following my previous notes to myself , there is a .map{ definition somewhere, where the HapMap position of a channel element is not given a variable name. However for teh life of me I cannot find where on earht this HapMap file is added to the reference indices.... so you guys need to find that and fix it, as this has come from you 😬 . Otherwise wierdly using the multiref CSV file (Rather than straight fasta), passes teh tests.

Should be fixed now, only needed to add the new reference sheet columns to the channel mapping adding a meta to the hapmap file. I also changed the test profile for angsd and mtnucratio CI tests to test_humanbam, so it will actually produce output. The hapmap will be properly integrated to the reference sheet in a separate PR

nf-core / eager