Chris Norman

Closing since I've cherry-picked everything to my working branch.

@shengzha Not yet, though I am working on it (this ticket will transition to the closed state when a fix has been merged). In the meantime if you have a...

@shengzha Not yet, though I am working on it (this ticket will transition to the closed state when a fix has been merged). In the meantime if you have a...

@shengzha In your case it looks like ApplyBQSR is failing because ALL of your input reads are being filtered out before BQSR ever sees them, due to having mapping quality...

I believe both `GatherVcfs` (picard) and `GatherVcfsCloud` (gatk) try to avoid doing any parsing at all if the shards are already block-gzipped - I believe they just transfer the blocks...

@ungwudik If I understand correctly, it sounds like publishing doesn't work at this time ? Why would we want to read from a repo if we can't publish other artifacts...

@ungwudik I see - thanks for the explanation - I didn't see anything mentioning that replication job. It might be helpful to include a comment in the build.gradle files in...

Rebased this to do some testing with current master.

@lbergelson I'm not sure - the change seems fine - although it will affect more than just Picard tool paths. It seems wrong as is though.

Yeah, thats not a helpful error message.