Open LucileSol opened 1 year ago
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
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 :
Or, one can use its own conda env for interproscan and add it to the custom.config :
And then run the pipeline the following way :