Pointing Cromwell to local EBS mounted storage on AWS Batch I'm trying to run the WDL tasks from the GTEx RNA-Seq pipeline with Cromwell using AWS Batch as a backend.
I store the STAR alignment index on an Elastic Block Store since my Cromwell server instance lacks sufficient disk space. The EBS Block is mounted to my Cromwell server at /data. The STAR index is located at /data/genomic-references/rnaseq/star_index_oh50.
Try as I might, I cannot get Cromwell to run the STAR task correctly.
My JSON inputs file:
 {
   &quot;rnaseq_pipeline_fastq_workflow.prefix&quot;: &quot;s3://mybucket/test/CL100148068&quot;,
   &quot;rnaseq_pipeline_fastq_workflow.star.fastq1&quot;: &quot;s3://anotherbucket/genotypedata/sample1.fq.gz&quot;,
   &quot;rnaseq_pipeline_fastq_workflow.star.star_index&quot;: &quot;/data/genomic-references/rnaseq/star_index_oh50/&quot;,
   &quot;rnaseq_pipeline_fastq_workflow.star.memory&quot;: &quot;32&quot;,
   &quot;rnaseq_pipeline_fastq_workflow.star.num_threads&quot;: &quot;4&quot;,
   &quot;rnaseq_pipeline_fastq_workflow.star.disk_space&quot;: &quot;200&quot;,
   &quot;rnaseq_pipeline_fastq_workflow.star.num_preempt&quot;: &quot;0&quot; 
 }

Error message:
tar: /data/genomic-references/rnaseq/star_index_oh50/: Cannot open: No such file or directory

Note that /data/genomic-references/rnaseq/star_index_oh50/ does exist and is readable.
The relevant command in the GTEx container is here:
tar -xvvf ${star_index} -C star_index --strip-components=1

If the files are stored locally, then why does tar fail to wrap the directory?
Somebody helped me with this one through other channels, but I wanted to make it publicly available:
Make a tarball of the STAR index. The option --strip-components=1 strips the first level of the path from the untarred items; thus, the expected tarball was made with something like
tar -cvf ${star_index} the_star_index_directory/

Then point Cromwell/WDL to the tarball, e.g. on S3. The GTEx container will unwrap the tarball on the fly during execution.