Currently, picard tasks within Skylab are using a picard version that is ~1yr old. One task has been modified to use a newer version, since the CLP it is calling is not present in the older versions. I had manually built + uploaded a picard image to quay to allow external users to use the pipeline, as the previous image was inacessible by some users. However, we should consider upgrading all tasks to use a newer picard version.
That being said, there are 2 considerations to keep in mind:
Should we really host our own version on quay, or can we use the official releases on Dockerhub?
Do we still need the R visualization packages in our version of Picard? (And if so, can we make the invocation a bit neater?)
Currently, picard tasks within Skylab are using a picard version that is ~1yr old. One task has been modified to use a newer version, since the CLP it is calling is not present in the older versions. I had manually built + uploaded a picard image to quay to allow external users to use the pipeline, as the previous image was inacessible by some users. However, we should consider upgrading all tasks to use a newer picard version.
That being said, there are 2 considerations to keep in mind:
Where to start:
library/tasks/Picard.wdl,docker/picard/Dockerfile, https://quay.io/repository/humancellatlas/secondary-analysis-picard?tab=tags, & https://hub.docker.com/r/broadinstitute/picard/builds . Relevant previous ticket: GL-473┆Issue is synchronized with this Jira Spike