Jeremiah H. Savage

The `merge_sqlite` tool of the GDC DNASeq workflow depends upon this feature: https://github.com/rabix/bunny/issues/193

The `picard_mergesamfiles` tool depends upon using `$(self.basename)` in the workflow ( https://github.com/NCI-GDC/gdc-dnaseq-cwl/blob/master/workflows/dnaseq/transform.cwl#L632 ). Issue filed as https://github.com/rabix/bunny/issues/197

The `samtools_idxstats_to_sqlite` tool depends upon a literal `valueFrom` passed to the metrics subworkflow: https://github.com/NCI-GDC/gdc-dnaseq-cwl/blob/master/workflows/dnaseq/transform.cwl#L603 Issue filed as https://github.com/rabix/bunny/issues/202

Thanks for testing. I currently don't see that branch on our repo: https://github.com/NCI-GDC/gdc-dnaseq-cwl/tree/feature/gdc (gives 404) The master branch should run transform.cwl without error using cwltool https://github.com/NCI-GDC/gdc-dnaseq-cwl/tree/master If you are familiar...

Ok. If you've found some fixes needed in the cwl, I'd certainly like to look at them for possible incorporation. For now, the below command is tested with work with...

@StarvingMarvin I reproduced your error. It was the same error I encountered here: https://github.com/rabix/bunny/issues/140 Which was fixed in the gdc cwl in this commit: https://github.com/NCI-GDC/gdc-dnaseq-cwl/pull/45 It looks like cwltool has...

bunny hangs when attempting to merge BAMs from multiple arrays. Issue filed as https://github.com/rabix/bunny/issues/215

@simonovic86 Fantastic! That fix also enabled me to run the transform to completion. I ran the bunny-generated metrics/sqlite file through a validator, which showed the BAM file contains the same...

@StarvingMarvin The docker image in this case is minimal: https://github.com/NCI-GDC/curl_docker/blob/master/Dockerfile I agree specifying this in cwl would probably be the best way to go. For now, I am able to...

@StarvingMarvin We have had to use host networking instead of bridge networking ever since switching to https://apt.dockerproject.org/repo/ instead of the older 1.6 docker in Ubuntu's Trusty. It seems to be...