dependabot-preview[bot] on maven
dependabot-preview[bot] on maven
Bump spring-boot-starter-parent… (compare)
dependabot-preview[bot] on maven
dependabot-preview[bot] on maven
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mr-c on maven
Add restart:always in docker-co… Merge branch 'main' into depend… (compare)
mr-c on cure-patch-1
mr-c on main
Add restart:always in docker-co… (compare)
Error: cwltool version failed to run on this workflow:
! Cwltool ran successfully, but an unexpected error occurred in CWLViewer!
Help us by reporting it on Gitter or a Github issue
hmm.. I get the same error as with cwltool --validate
really.
Viewer:
Tool definition failed validation:
../data/git/aa420273539ad7bcf384c37614f6f636810042f2/Workflows/bams2gvcf.woBQSR_male_chrXY_wXTR.cwl:170:16: Workflow step output 'vcf_tbi' does not correspond to
../data/git/aa420273539ad7bcf384c37614f6f636810042f2/Tools/gatk3-HaplotypeCaller-XCORE1-ploidy1.cwl:51:1: tool output (expected 'vcf', 'log')
Command line:
(base) stain@biggie:~$ cwltool --validate https://raw.githubusercontent.com/ddbj/human-reseq/master/Workflows/bams2gvcf.woBQSR_male_chrXY_wXTR.cwl
/home/stain/miniconda3/bin/cwltool 1.0.20190228200117
Tool definition failed validation:
https://raw.githubusercontent.com/ddbj/human-reseq/master/Workflows/bams2gvcf.woBQSR_male_chrXY_wXTR.cwl:170:16: Workflow step output 'vcf_tbi' does not correspond to
https://raw.githubusercontent.com/ddbj/human-reseq/master/Tools/gatk3-HaplotypeCaller-XCORE1-ploidy1.cwl:51:1: tool output (expected 'vcf', 'log')
https://img.shields.io/badge/cwl-valid-B5314C.svg?logo=common-workflow-language
but the viewer would need to have an in-between resource that checks it live.
sbg: 'https://sevenbridges.com'
raised as DataBiosphere/topmed-workflows#97 although there is some other bug as https://view.commonwl.org/workflows/github.com/stain/topmed-workflows/blob/namespaces/aligner/sbg-alignment-cwl/topmed-alignment.cwl# turns out empty - seems to be because id
confuses the CWL Viewer :(
https://view.commonwl.org/workflows/github.com/stain/topmed-workflows/blob/no-id/aligner/sbg-alignment-cwl/topmed-alignment.cwl works when I deleted id
as well
/tmp
had ran out again and the cronjob had failed.. because there was no disk space for docker-compose to do exec
! (why!?)
docker-compose exec -T spring find /tmp -type f -mtime +1 -delete
docker-compose exec -T spring find /tmp -type d -mtime +30 -delete
it's basically deleting the RO-Crate directories (which have been zipped) - that's a bug. But the big one is the temporary git clones because the "main" git checkout is locked. This happens when someone loads a large multi-GB repository and gets tired of it being slow and click Refresh - basically they are then causing a concurrency conflict against themselves..