bunny

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It is really hard to find which tool in the workflow failed. Can you make this available in bunny output log?

vladimirkovacevic

Add dry run mode

1

Similar to `make -n`, it would be nice to have a 'dry run' mode where Bunny does not actually execute anything but just prints statements it would execute. My use...

Gig77

Usage examples on help page

1

Couple of bunny usage examples in the 'rabix --help' output would be helpful to get the syntax quicker. Took me a bit to figure out the exact command line syntax...

Gig77

bcbio scaling tests: Docker required, stdout/stderr buffer, many parallel jobs

2

Thank you for all the help on getting bcbio running with our test CWL (#94). We've revamped how bcbio runs the CWL to avoid all the command line issues we...

chapmanb

Inconsistency between reame.md and information output from ./rabix -h"

4

Entering "./rabix -h" presents the command as rabix [OPTION]... [-- {inputs}...] whereas readme.md presents it as ./rabix [OPTIONS] I'd say `` was a more accurate name than ``, as Rabix...

Titch990

Workflow outputs

2

When running local Bunny executor on workflow (let's say workflow has many tools and outputs) how can I collect all output files?

vladimirkovacevic

With cwltool, I am able to use urls as workflow and job input, as in: ``` mkdir tmp cache cwltool --tmpdir-prefix tmp/ --cachedir cache/ https://raw.githubusercontent.com/NCI-GDC/gdc-dnaseq-cwl/master/workflows/dnaseq/etl_http.cwl https://raw.githubusercontent.com/NCI-GDC/gdc-dnaseq-cwl/master/workflows/dnaseq/etl_http_NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.json ``` The cwltool fetcher...

jeremiahsavage

sivkovic

sinisa88

TES: use protobuf/grpc generated client

1

The task execution schemas are defined in protobuf and gRPC, which gives us the ability to generate client code. Would you guys like to use this instead of maintaining your...

buchanae