Bioconda env for interproscan not working for the functional_annotation subworkflow

[LucileSol]

The bioconda env for interproscan is not working in the functional_annotation subworkflow.

To use interproscan, one needs to install the tool and database locally and add a similar line to a custom.config :

env.PATH ='${PATH}:/projects/interproscan/interproscan-5.59-91.0'

Or, one can use its own conda env for interproscan and add it to the custom.config :

process {
    withName: 'INTERPROSCAN' {
        conda = '/sw/anaconda/2019.10/envs/interproscan'
        container = null
    }    
}

And then run the pipeline the following way :

nextflow run NBISweden/pipelines-nextflow -profile singularity -params-file params.yml -c custom.config