I inserted an upstream stage in the gCNV pipeline which sets a specific sample ordering, so that all joint-calling and unpacking is done using a fixed SG ID order.
This stage didn't return the expected output paths, so during the first run for a group of samples, the SGID ordering is set, but the rest of the setup fails. The gCNV pipeline has to be started twice. This should patch that...
I've chucked a bunch of reformatting here, but the meaningful change is on line 41. The rest is just line-length changes
I inserted an upstream stage in the gCNV pipeline which sets a specific sample ordering, so that all joint-calling and unpacking is done using a fixed SG ID order.
This stage didn't return the expected output paths, so during the first run for a group of samples, the SGID ordering is set, but the rest of the setup fails. The gCNV pipeline has to be started twice. This should patch that...
I've chucked a bunch of reformatting here, but the meaningful change is on line 41. The rest is just line-length changes