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shard_test example wdl needs updating for jgi

Describe the bug The jaws-sharding example in jaws-tutorial-examples repo fails when run on JGI because it has commands section with shifter commands in the shard_test.wdl. wdl needs to be updated to run on JGI.

To Reproduce

git clone https://code.jgi.doe.gov/advanced-analysis/jaws-tutorial-examples.git
cd jaws-sharding
jaws run submit shard_test.wdl shard.json out jgi

Expected behavior jaws-sharding example should run on both cori and jgi sites

Screenshots from shard_test.wdl

    command {
        set -e -o pipefail
        shifter --image=jfroula/jaws-sharding:1.0.10 fastq_indexer.py --input ${reads} --output ${bname}.index

        shifter --image=jfroula/jaws-sharding:1.0.10 create_blocks.py -if ${bname}.index -ff ${reads} -of ${bname}.sharded -bs ${chunk_size}
    }

Specs (please complete the following information):

  • JAWS Site: jgi
  • Version 2.1

Additional context I'm wondering if I should put issues about jaws-tutorial-examples repo in that repo rather than here. My fear is that they may be forgotten there, since we don't normally look there for issues.