Closed dwaggott closed 9 years ago
chapmanb
commented
9 years ago Daryl;
Sorry about the issue. I tried to reproduce this with the test case (./run_tests.sh joint) but couldn't. Is it possible you have joint calling specified but don't have the samples in a shared batch within the metadata? I'll try to think more on possible issues but that's the first that comes to mind. Hope this explains it.
dwaggott
commented
9 years ago Ugh, I sure am good at doing everything wrong.
I put batch in the sample.csv file but forgot to add it to the template config yaml. It needs to be in both to end up in the final sample yaml, correct?
On Thu, Mar 19, 2015 at 6:05 PM, Brad Chapman notifications@github.com wrote:
Daryl; Sorry about the issue. I tried to reproduce this with the test case (./run_tests.sh joint) but couldn't. Is it possible you have joint calling specified but don't have the samples in a shared batch within the metadata? I'll try to think more on possible issues but that's the first that comes to mind. Hope this explains it.
— Reply to this email directly or view it on GitHub https://github.com/chapmanb/bcbio-nextgen/issues/794#issuecomment-83834774 .
dwaggott
commented
9 years ago Where does batch come into play for the joint pipeline. If it didn't make it into the final yaml, could I start the pipeline at the gemini time point?
On Fri, Mar 20, 2015 at 2:55 PM, Daryl Waggott dwaggott@gmail.com wrote:
Ugh, I sure am good at doing everything wrong.
I put batch in the sample.csv file but forgot to add it to the template config yaml. It needs to be in both to end up in the final sample yaml, correct?
On Thu, Mar 19, 2015 at 6:05 PM, Brad Chapman notifications@github.com wrote:
Daryl; Sorry about the issue. I tried to reproduce this with the test case (./run_tests.sh joint) but couldn't. Is it possible you have joint calling specified but don't have the samples in a shared batch within the metadata? I'll try to think more on possible issues but that's the first that comes to mind. Hope this explains it.
— Reply to this email directly or view it on GitHub https://github.com/chapmanb/bcbio-nextgen/issues/794#issuecomment-83834774 .
chapmanb
commented
9 years ago Daryl;
Putting the batch in the sample.csv should be all you need to do, and it'll end up in the final sample YAML. I couldn't reproduce an issue with it being left out running the unit test (./run_tests.sh template) but please let me know if I'm missing anything.
Regarding re-running, you'll need to re-do the joint and GEMINI analysis, so remove both of those directories and checkpoints/multicores2.done and you should be able to re-run. Hope this fixes it for you.
My gemini directory (joint calling n=24) has vcf's and db's for each sample. In past runs it only contained the multisample vcf and db. Also, each of these db's was put into the final directory. Does that seem expected? The pipeline was restarted so it could have been a failure somewhere.
i.e.