Catch error case where 0 reads pass filtering and params.ignore_failed_trimming = True

sminot commented 1 year ago

In my use of this workflow I found an edge case where the filtering step produces 0 reads. In those cases when params.ignore_failed_trimming = True, those samples should be ignored. However, instead I observed that the workflow failed with:

Missing output file(s) `*.filt.fastq.gz` expected by process NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM

By adding the optional flag to the output using params.ignore_failed_trimming, this error will be avoided only in those cases when it satisfies the request of the user.

My apologies for not adding tests, but this is such a small change that I thought it might be acceptable.

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 - have you followed the pipeline conventions in the contribution docs
[ ] If necessary, also make a PR on the nf-core/ampliseq branch on the nf-core/test-datasets repository.
[ ] Make sure your code lints (nf-core lint) (this failed, but not in any part of the code that I touched)
[x] Ensure the test suite passes (nextflow run . -profile 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 year ago

This PR is against the `master` branch :x:

Do not close this PR
Click Edit and change the base to dev
This CI test will remain failed until you push a new commit

Hi @sminot,

It looks like this pull-request is has been made against the sminot/ampliseq master branch. The master branch on nf-core repositories should always contain code from the latest release. Because of this, PRs to master are only allowed if they come from the sminot/ampliseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions[bot] commented 1 year ago

`nf-core lint` overall result: Failed :x:

Posted for pipeline commit d963baf

+| ✅ 143 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   3 tests had warnings |!
-| ❌   8 tests failed       |-

### :x: Test failures: * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable not found: `params.validationShowHiddenParams` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable not found: `params.validationSchemaIgnoreParams` * [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/ISSUE_TEMPLATE/bug_report.yml` does not match the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/nf-core-ampliseq_logo_light.png` does not match the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `lib/NfcoreTemplate.groovy` does not match the template * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `schema_ignore_params` from `nextflow config` not found in nextflow_schema.json * [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'. ### :heavy_exclamation_mark: Test warnings: * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``manifest.version`` should end in ``dev``: ``2.6.1`` * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README did not have a Nextflow minimum version badge. * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Parameter `input` is not defined in the correct subschema (input_output_options) ### :grey_question: Tests ignored: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `conf/igenomes.config` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.gitattributes` * [actions_ci](https://nf-co.re/tools-docs/lint_tests/actions_ci.html) - actions_ci ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - 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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) - 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`.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) - `.github/workflows/linting.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/email_template.html` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/email_template.txt` 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) - `docs/images/nf-core-ampliseq_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `docs/images/nf-core-ampliseq_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_awstest](https://nf-co.re/tools-docs/lint_tests/actions_awstest.html) - 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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 2.9 * Run at `2023-09-19 16:51:38`

d4straub commented 1 year ago

Hi there,

thanks for providing a fix! I havent come across that case yet. However, I have concerns with this PR.

the change was added to the master branch, but except the CHANGELOG conflicts that might work anyway.
params.ignore_failed_trimming is supposed to be a param for cutadapt, e.g. when after cutadapt the number of reads fall below a threshold (--min_read_counts, default: 0), but I agree the naming is ambiguous so that could be also used here
there isnt any notification when a sample fails the threshold and params.ignore_failed_trimming = true, it just continues silently, right? That is a little concerning but probably also fine.
if that error occurs, as you have described above, there is no indication that this could be solved by using --ignore_failed_trimming, correct? I think thats maybe the most severe problem. When the problem occurs its not clear that there is a solution at hand.

So the optimal solution to me seems at that point that (1) there is a hint when an error occurs at that step to use a specific parameter, probably mentioning the samples that failed, (2) when the parameter is used a warning lists samples that failed but the pipeline continues. Essentially how https://nf-co.re/ampliseq/2.6.1/parameters/#ignore_empty_input_files & https://nf-co.re/ampliseq/2.6.1/parameters/#ignore_failed_trimming work. My idea would be to create empty output files when there is none produced by the filtntrim command and then filter the outgoing channel with nextflow's .branch. Would that make sense?

d4straub commented 1 year ago

As a note, this is easily reproducible by running nextflow run nf-core/ampliseq -r 2.6.1 -profile test,singularity --outdir results --trunclenf 300 --trunclenr 300 where trunclenf/r will cause discarding all reads because its PE250.

sminot commented 1 year ago

I really appreciate your taking a look at this PR, @d4straub , and I must apologize for not putting it together as thoroughly as I should have. The nf-core/ampliseq workflow is really amazingly helpful, and I appreciate all the work that you all have put into it.

I'm trying to come up with a test case that recapitulates my experience in which 0 reads are output by the DADA2_FILTNTRIM process, such that no files are created and the process ends with an error. I'm getting the test suite all staged and running on my local system, and I'll see if I can find the right kind of inputs which sufficiently resemble this particular (admittedly extremely low quality) dataset.

I like your idea of using empty outputs from the process, since that would ensure that the dropped samples are still logged as being missing in the same way that the current skipping behavior will document. Given the utility of this workflow, I think it will be worthwhile to add that particular feature.

I'll work on getting that running using a new test dataset which is appropriate for this edge case. I'll update you when I have something pushed that is ready for your inspection.

d4straub commented 1 year ago

Thanks! I was testing a little bit and actually, the solution of https://nf-co.re/ampliseq/2.6.1/parameters/#ignore_empty_input_files & https://nf-co.re/ampliseq/2.6.1/parameters/#ignore_failed_trimming, i.e. having a verbose error, having an empty file and filtering it with .branch, reporting samples and warnings, went fine until it clashed in:

https://github.com/nf-core/ampliseq/blob/b602d1908ac7d43c71624526990c7c43a8ade45f/workflows/ampliseq.nf#L343-L347 where it couldnt .join, because sample ids, which are in meta.id, didnt match (because some samples were removed!)
after removing meta.id, the pipeline failed in a subsequent step where meta.id was required (dont have my notes with me, not sure it was, some sort of merging in R where cbind failed because of missing columns, i.e. samples...)

at that point I found it got too complicated. So probably that approach is not perfect in that case. But I definately didnt come up with an elegant solution. Probably you do it better, just wanted to share my failed attempt that you might benefit from it ;)

sminot commented 1 year ago

This is actually really relevant @d4straub, since I'm trying to debug a dataset which stops at basically the exact point you describe, but which I thought should still pass filtering for at least some samples.

I'm doing more local testing, and I'll see if I can figure this one out and propose a good fix.

sminot commented 1 year ago

Closing in favor of https://github.com/nf-core/ampliseq/pull/641

nf-core / ampliseq