genome-manager/main.nf at main · pfizer-opensource/genome-manager · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
#!/usr/bin/env nextflow

nextflow.enable.dsl=2

if (params.command == 'register-genome') {
    include { ADD_GENOME } from './workflows/add_genome'
}
else if (params.command == 'register-gene') {
    include { REGISTER_USER_DEFINED_GENE } from './workflows/register_user_defined_gene'
}
else if (params.command == 'update-gene') {
    include { UPDATE_USER_DEFINED_GENE } from './workflows/update_user_defined_gene'
}

workflow {
    WorkflowMain.initialize(workflow, params, log)
    WorkflowAddGenome.initialize(params, log)

    if (params.command == 'register-genome') {
        ADD_GENOME()
    }
    else if (params.command == 'register-gene') {
        REGISTER_USER_DEFINED_GENE()
    }
    else if (params.command == 'update-gene') {
        UPDATE_USER_DEFINED_GENE()
    }
}

// workflow {
//     GENOME_MANAGER()
// }