Closed ramprasadn closed 4 months ago
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 |!
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]
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.
Here are the emitted arguments. Maybe a typo for gvcf_tbi
?
Need to run for a meeting now, will continue testing (and checking the case error) later today
Here are the emitted arguments. Maybe a typo for
gvcf_tbi
?
indeed looks like a typo. Thanks for testing and reporting
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.
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]
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).