Tower run on isoseq full test data set fails

[taylorreiter]

This is the email log I receive. I don't really understand why this is working for the small test data set but failing with a real data set.

This is the input samplesheet: https://raw.githubusercontent.com/Arcadia-Science/test-datasets/ter/seqqc-full/seqqc/samplesheet_isoseq.csv

Execution completed unsuccessfully!

The full error message was:

Error executing process > 'ARCADIASCIENCE_SEQQC:SEQQC:MULTIQC'

Caused by:
  Invalid AWS Batch job definition -- provide a Docker image name or a Batch job definition name

Command executed:

  multiqc \
      --force \
       \
      --config multiqc_config.yml \
       \
      .

  cat <<-END_VERSIONS > versions.yml
  "ARCADIASCIENCE_SEQQC:SEQQC:MULTIQC":
      multiqc: $( multiqc --version | sed -e "s/multiqc, version //g" )
  END_VERSIONS

Command exit status:
  -

Command output:
  (empty)

Work dir:
  s3:// {{ * }} /scratch/3q0IOloBnLohWg/ab/21102db37f0b79009b6c7ce97bbf14

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

[taylorreiter]

As explained by @mertcelebi, this was caused by not specifying "docker" as the config profile. Here's the slack message mert sent me:

Here’s why:

• So the error message says: “you haven’t provided a valid container image for AWS Batch to spin up an instance”
• Before your change here, you generally seem to run your pipelines without the --docker flag. That worked when the default behavior was checking if the containerEngine was singularity or not (the original MultiQC container check). But now, you check equality of containerEngine to docker. And because you don’t run it with the --docker flag, it fails, so the AWS Batch doesn’t find your container.

If you re-run with the docker profile, it should work