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GenomicsDBImport creates DB with limited file permissions

WhargreaWhargrea GuelphMember
edited November 2019 in Ask the GATK team

I am running the GATK4 best practices pipeline for germline variant discovery in a custom Nextflow pipeline. When I run GenomicsDBImport it creates the DB in the Nextflow work directory. I want to move this DB out of the work directory to a directory of my choosing using the publish option in Nextflow. This is so that I can add to the DB as I process more samples instead of creating the thing from all samples available every time I run. However, the DB has file permissions drwx------. which prevents me from moving the DB as a measly user. Is there a way to create the directory such that a user can move it? I can't find a command-line option for this.


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