julesjacobsen / exomiser-test-nf Goto Github PK

If a relative path is provided, it is possible that Exomiser is trying to infer the absolute path but prepending the provided path with the absolut path of the directory where Exomiser is running from.

Inside the Nextflow process script, we only have access to the basename of the exomiser-data directory.
To find the directory we can use the unix command readlink -f (Stack Overflow reference) to capture the full path in a bash variable and provide it to exomiser.

The code could look like this:

ch_exomiser_data_path = Channel.fromPath("${params.exomiser_data_path}")
// Define Process
process run_exomiser {
    input:
    ...
    file(exomiser_data_path) from ch_exomiser_data_path

    output:
    ...

    script:
    """
    ABSOLUTE_EXOMISER_DATA_PATH=`readlink -f ${exomiser_data_path}`
    exomiser-cli  \
     --analysis exomiser_analysis.yml  \
     --spring.config.location=${template_application_properties}
     --exomiser.data-directory=\$ABSOLUTE_EXOMISER_DATA_PATH
     --exomiser.${params.assembly}.data-version=${params.assembly_data_version}
     --exomiser.phenotype.data-version=${params.phenotype_data_version}
    """
  }

NOTE:
Q: Why do we need to escape the dollar in this case --exomiser.data-directory=\$ABSOLUTE_EXOMISER_DATA_PATH?

A: Nextflow reserves the dollar for groovy variables. We created a bash variable with the snippet

ABSOLUTE_EXOMISER_DATA_PATH=`readlink -f ${exomiser_data_path}`

To use a bash variable within the script directive of a Nextflow process, escaping the $ with a backslash is required so that the variable is correctly evaluated as a bash variable and not groovy.