Brad Chapman

pca sklearn failure in latest development version

10

Brent; We've been trying to use the latest development in bcbio (to get the initial hg38 support) and running into a failure during pca. Is there a minimum number of...

HTTP input file names not respected in execution VM

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Hi all; In testing release 35 with CWL inputs I've also been looking at supporting remote URL references. This is working correctly for GS URLs but not for http URLs....

Provide genotypes (GT) for somatic variant calls

9

Chris and Sangtae; This is a follow-up to a bcbio discussion (https://github.com/chapmanb/bcbio-nextgen/issues/2112#issuecomment-338307641) which I thought could use it's own thread. In bcbio we're converting `NT` and `SGT` into FORMAT genotypes...

smoove germline validations with Genome in a Bottle NA24385

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Brent; Thanks again for all the help getting smoove working. I've got a branch that includes it and have been running validations comparing to the lumpyexpress based approach using the...

bunny 1.0.3 resolving relative file paths from step directory

2

Milos and all; I've been testing the 1.0.3 release with the fixed permissions issues for #325 -- thank you for these -- and am running into an issue with relative...

Permissions error writing `cwl.outputs.json` when running with Docker

4

While testing the latest bcbio test CWL workflow (https://github.com/bcbio/test_bcbio_cwl) using the 1.0.1 release, I'm running into a permissions issue using a Docker container. Everything runs cleanly when using `--no-container` but...

Thanks for all the work on cached workflows in the latest 1.0.2 release. I'm excited to see this feature get additional development, it's very important to our use cases where...

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...

Fixes for regional BAM re-alignment with bgzipped inputs: glia: out_of_range and tabix errors

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Eric; This fixes two issues I ran into while using glia for realignment included called variants. - It avoid erroring out when tabix region retrieval has no variants. The current...

German; @ameynert reported an issue using bamsormadup for a deep WGS sample within bcbio. We're running bamcat and bamsormadup on a split set of alignment BAMs to generate a final...