Avoid re-doing STAR references in RNAseq Germline variant workflow
AnsweredHow do I stop STAR from generating a new reference each time the workflow is run on a sample?
Everytime I run gatk4-rnaseq-germline-snps-indels for each sample, the STAR reference step is created again. I believe this is the case because each run is an independent cromwell-execution. Is there something I'm missing or should I "adapt" the workflow to check for the file and re-use if already present?
This is the source for the aforementioned issue:
Another question, for some files in the output (inside cromwell-executions), the owner is me who ran the workflow, and for some is the root (which docker runs as). However, I don't have root access on this particular server, I'm only a user belonging to the docker group. Then, how can I access these files or change their permission? Is this possible?
Thank you
-
Hi ThyagoLC,
I am going to move your post into our Community Discussions -> General Discussion topic, as the germline topic is for reporting bugs with GATK.
You can read more about our forum guidelines and the topics here: Forum Guidelines.
Best,
Pamela
-
Hi ThyagoLC,
If you take a look at this line in the WDL, the StarGenerateReferences task runs if the input zippedStarReferences is undefined. So if you already have a reference file you'd like to use, you can pass that to the zippedStarReferences input.
As for your second question, I'm not sure if this is the right forum for it. We support questions/issues related to Terra Cromwell, but not external/personal instances of Cromwell. Bioinformatics StackExchange and Cromwell Slack are the best resources for those questions.
Best,
Samantha
-
I found out about the zippedStarReferences input later on, thank you!
As for the second question, I'll leave my solution below so others may benefit from it:
I used a custom .conf file to pass my user/group UID:GID to docker in the following place:
Then, just ran the custom.conf to my call
java -Dconfig.file=/path/to/custom.conf cromwell.jar ...
Thank you.
-
Hi ThyagoLC,
Thanks for following up and posting your solution!
Best,
Samantha
Please sign in to leave a comment.
4 comments