cromwell docker scripts cannot handle containers with entry points well

I noticed that if I give cromwell a container with existing entry-point (like quay.io/ucsc_cgl/fastqc@sha256:86d82e95a8e1bff48d95daf94ad1190d9c38283c8c5ad848b4a498f19ca94bfa , for instance) and give a file as an input it (both develop branch and latest release) fails to run the entry point properly. Here is an example of task

task report {

  String fileName
  File file

  command {
    ${file}
  }

  runtime {
    docker: "quay.io/ucsc_cgl/fastqc@sha256:86d82e95a8e1bff48d95daf94ad1190d9c38283c8c5ad848b4a498f19ca94bfa"
    #docker: "quay.io/biocontainers/fastqc@sha256:bb57a4deeec90633e746afbc38c36fdb202599fe71f9557b94652e9c8f3c1a02"
  }

  output {
    #File out = sub(file, "\\.fastq.gz", "_fastqc.gz")
    File out = "${fileName}.fastqc.gz"
  }
}

[dinvlad]

I think it is not longer relevant

Could you elaborate? We still can’t use images that have ENTRYPOINT set.

[geoffjentry]

@cjllanwarne I can’t find it now (perhaps it has since been closed as a won’t fix) but this has come up before. If you’re open to trying to track it down close one as a dupe.