Hello there,
I’ve multiple workflows and each workflow has different processes.
After I’m through with two workflows I’m interested in integrating output from different steps of these workflows.
I’d like to have a workflow, say named as integrate. In this integrate I’d like to put different processes such as combine_p1_p2, combine_p3_p4.
I’ve main.nf as:
include { rna } from './workflows/rna'
include { wes } from './workflows/wes'
include { integrate_RNA_WES} from './workflows/integrate'
workflow {
if (params.analysis=="both"){
wes()
rna()
wes.out.parsed_cnv.view()
rna.out.merged_rdata.view()
}
}
In integrate workflow, I’d like to put few processes. These are mostly custom scripts.
In integrate workflow I’ve:
include {integrate_parsed_CNV_merged_RNA } from '../modules/integrate/processes_integrate.nf'
workflow integrate_RNA_WES {
integrate_parsed_CNV_merged_RNA()
}
I’ve processes_integrate.nf as:
process integrate_parsed_CNV_merged_RNA {
input:
output:
script:
"""
"""
}
process integrate_files_diff {
input:
output:
script:
"""
"""
}
How do I call integrate_parsed_CNV_merged_RNA of integrate.nf once I’ve output from wes’s parsed_CNV and rna’s merged_feature?
Sorry this may seem complicated and confusing.