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sanger-tol / treeval

Pipelines for the production of Treeval data
https://pipelines.tol.sanger.ac.uk/treeval
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Pre tag #132

Closed DLBPointon closed 1 year ago

DLBPointon commented 1 year ago

Pre-release PR

Talking with @priyanka-surana , we only need to get testing up and running (+ zenodo) and then we are ready for release.

To get that sorted i've been told to rope you in @muffato

github-actions[bot] commented 1 year ago

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

Posted for pipeline commit 6328583

+| ✅ 125 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗   8 tests had warnings |!
### :heavy_exclamation_mark: Test warnings: * [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: `.github/workflows/awstest.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found: `.github/workflows/awsfulltest.yml` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``manifest.version`` should end in ``dev``: ``'1.0.0'`` * [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 `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 `methods_description_template.yml`: _## Update the HTML below to your prefered 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 WorkflowTreeval.groovy: _System.exit(1)_ [line 17] ### :grey_question: Tests ignored: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `assets/nf-core-treeval_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `conf/test_full.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-treeval_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - 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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.show_hidden_params` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.schema_ignore_params` * [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) - 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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) - `.github/.dockstore.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) - 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'.github/workflows/ci.yml' checks minimum NF version * [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 (230 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/yaml' * [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: fix-linting.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: linting_comment.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: linting.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 '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 `2023-09-19 08:34:19`
DLBPointon commented 1 year ago

Hi @muffato , again thanks for the code. I've attributed the changes to you.

Changes to the stats collection work and avoid any red lettered errors. Only issue is that because this is technically pre-workflow completion, we no longer have pipeline completion time and pipeline execution time. However, I should be able to time stamp that point and calculate what I need as it is practically completed. This isn't currently needed for the graphs I'm making so I'm happy to leave that for 1.0.1

Pipeline at this point has been tested on farm in full and rapid modes on the OschSubset data.

Both took 25 mins using whatever resources they wanted. I'll test this using the GitHub resource limits.

I've created 4 test profiles, 2 full Osc dataset test for on the farm and 2 subset data for GitHub runner.

How should I set up the data for these? I have an s3 bucket containing a very minimal set for the BGAcademy based on nxOscSubset.

Should we have a data download step to set up the gene alignment and busco data?

I'll sort the linting too.

DLBPointon commented 1 year ago

I've just tested the pipeline locally using the github settings, but the cram_et_al module refuses to run. I'm assuming the restriction on resources is too much and it just silently dies.

Command in use is:

bsub -Is -tty -e error -o out -n 2 -q oversubscribed -M4000 -R'select[mem>4000] rusage[mem=4000] span[hosts=1]' 'nextflow run main.nf -profile github_rapid,singularity --input assets/local_testing/nxOscSUBSET.yaml --outdir OscSUBSET-TEST -entry RAPID'

Everything runs fine using non github profiles

muffato commented 1 year ago

Hi,

I can confirm that the farm_* profiles work locally 👍🏼

There's an issue with the github_* profiles: they seem to be missing some of the keys the farm_* profiles have:

$ nextflow run ../src/sanger-tol/treeval/ -entry RAPID -profile github_rapid,singularity
ERROR ~ Cannot get property 'lineage' on null object

 -- Check script '/lustre/scratch123/tol/teams/tolit/users/mm49/nextflow/src/sanger-tol/treeval/./workflows/../subworkflows/local/yaml_input.nf' at line: 99 or see '.nextflow.log' file for more details
ERROR ~ Cannot get property 'teloseq' on null object

 -- Check script '/lustre/scratch123/tol/teams/tolit/users/mm49/nextflow/src/sanger-tol/treeval/./workflows/../subworkflows/local/yaml_input.nf' at line: 92 or see '.nextflow.log' file for more details

Finally, in my tests, the results/treeval_info/TreeVal_run_Oscheius* files only have a few lines under RESOURCES. They're meant to have the complete trace file, aren't they ? It feels like Nextflow had not finished writing / closed the trace file when TreeVal opened it for reading and copying.

EDIT: I checked out the code yesterday afternoon, so didn't test the changes you pushed this morning.

DLBPointon commented 1 year ago

The github profiles weren't working yesterday as they were waiting on the new data set.

I've set a couple of jobs running over night so i'll have a look in the morning about the summary file output.

For now, CI works!

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DLBPointon commented 1 year ago

At this point, I believe the code is stable and tests will pass. However, we've realised that documentation needs to be improved. We are working on this now and hope to have a substantial amount done to day ready for merge and hopefully tagging. closes #138

priyanka-surana commented 1 year ago

Awesome job getting the tests to work.

DLBPointon commented 1 year ago

Hi @muffato and @priyanka-surana,

We now believe TreeVal is now ready for a full review. We have now completed pre-pipeline data prep, adding the BGA23 gitpod.yaml, fixing the TreeValProject.summary (to a usable state, there are unfortunate limitations) and generally fixed it up.

Thanks.

priyanka-surana commented 1 year ago

A general suggestion for the website is to use full urls rather than relative paths.

muffato commented 1 year ago

Links to markdowns within the same directory (i.e. docs/) should work, but let's check once everything is on dev/the pipeline website

DLBPointon commented 1 year ago

Here are some suggestions about the documentation. See #140 for a couple of code suggestions.

Also, before merging dev into main I'd very much like to see how the documentation looks like on the pipelines website, especially the fact there are more files than just usage.md and output.md.

I've actioned everything now, merged your code suggestions, and tested everything. Thanks for the help.

DLBPointon commented 1 year ago

Prettier failing due to odd number of underscores....

This leaves us with a file called `bTaeGut1_4.fasta` the genomic assembly of bTaeGut1_4 (the [Tree of Life ID](https://id.tol.sanger.ac.uk/) for this species) also known as _Taeniopygia guttata_, the Australian Zebrafinch.
muffato commented 1 year ago

Prettier failing due to odd number of underscores....

Try escaping the one inside the assembly names with \ ?

DLBPointon commented 1 year ago

Prettier failing due to odd number of underscores....

Try escaping the one inside the assembly names with \ ?

Fixed, escaping wouldn't work. It would get "corrected". I've instead put the assembly name inside of backticks. Which also signifies importance so win-win.