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Published 20 hours ago • verified publisher icon nf-core

Patch

Open ramprasadn opened this issue 10 months ago • 5 comments

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
  • [ ] If necessary, also make a PR on the nf-core/raredisease 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 --outdir <OUTDIR>).
  • [ ] Ensure the test suite passes (nextflow run . -profile test_one_sample,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).

ramprasadn avatar Apr 16 '24 11:04 ramprasadn

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

Posted for pipeline commit 9da1d8d

+| ✅ 183 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

:grey_question: Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • modules_config - modules_config

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-17 08:44:15

github-actions[bot] avatar Apr 16 '24 11:04 github-actions[bot]

The test profile works perfectly for this patch branch on RHEL 9 and Fedora 39 with singularity and local executor (no executor/cluster setting). [I am testing 2.0.1 with a full-scale dataset and will also test the patch branch, if it can complete in time]

fa2k avatar Apr 17 '24 13:04 fa2k

Hi! I am trying out running this patch PR on the dataset I have been running before (i.e. GIAB on our server).

I run into errors, trying to see whether they are on my part or in the code.

ERROR ~ Cannot get property 'case_id' on null object

 -- Check script '<path>/raredisease/./workflows/raredisease.nf' at line: 166 or see '.nextflow.log' file for more details
ERROR ~ No such variable: Exception evaluating property 'gtbi' for nextflow.script.ChannelOut, Reason: groovy.lang.MissingPropertyException: No such property: gtbi for class: groovyx.gpars.dataflow.DataflowBroadcast

 -- Check script '<path>/raredisease/./workflows/../subworkflows/local/call_snv.nf' at line: 77 or see '.nextflow.log' file for more details

In a quick look it indeed looks like there is a mismatch for the Sentieon workflow.

Here is what is asked for from the "parent" processes using the Sentieon SNV calling subprocess.

https://github.com/nf-core/raredisease/blob/d0b512be4b6c542fa8537ea508e7f931e4dab491/subworkflows/local/call_snv.nf#L77

Here are the emitted arguments. Maybe a typo for gvcf_tbi?

https://github.com/nf-core/raredisease/blob/d0b512be4b6c542fa8537ea508e7f931e4dab491/subworkflows/local/variant_calling/call_snv_sentieon.nf#L124-L129

Need to run for a meeting now, will continue testing (and checking the case error) later today

Jakob37 avatar Apr 18 '24 08:04 Jakob37

Here are the emitted arguments. Maybe a typo for gvcf_tbi?

indeed looks like a typo. Thanks for testing and reporting

jemten avatar Apr 18 '24 13:04 jemten

Quick update. I am running into more downstream issues, but I think these are on my side. I will continue working through the GIAB run and raise any issues I find, but will probably complete when you are done with this PR.

I would like to run the test data, but we have an offline-only server, and it is not feasible to pull all containers to my local computer.

Jakob37 avatar Apr 19 '24 14:04 Jakob37

I've tested the most recent version of this PR and I do get an error. I made a separate issue because I also get the error in pipeline version 2.0.x #542 . The error is this:

[a8/b58d57] NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_INDEX_SPLIT_ALIGNMENT (NA12878)          [100%] 25 of 25, cached: 25 ✔

Join mismatch for the following entries:
- key=[id:NA12878, sample:NA12878, lane:1, sex:2, phenotype:2, paternal:0, maternal:0, case_id:NA12878, num_lanes:1, read_group:'@RG\tID:NA12878\tPL:illumina\tSM:NA12878', single_end:false, interval:chr13, nr_of_intervals:25] values=[/data0/paalmbj/na12878_med_pipeline/work/83/20f04adedf5dc4bb5ee4b6b85e262c/NA12878_chr13.bam, /data0/paalmbj/na12878_med_pipeline/work/d0/156dd6f94e30b5c404ec292aad5b8c/NA12878_chr13.bam.bai]

fa2k avatar May 13 '24 00:05 fa2k