Parabricks-Genomics-nf/nextflow.config at main · Sydney-Informatics-Hub/Parabricks-Genomics-nf · 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
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
// Define some metadata for publishing pipeline on GitHub
manifest {
    author = 'Georgie Samaha, Sydney Informatics Hub, University of Sydney'
    name = 'Genomics001: Parabricks-Genomics-nf'
    description = 'GPU-enabled mapping and short variant calling with Parabricks'
    homePage = 'https://github.com/Sydney-Informatics-Hub/Parabricks-Genomics-nf'
}

// Mandate a minimum version of nextflow required to run the pipeline
nextflowVersion = '!>=20.07.1'

// Set default workflow parameters
// See https://www.nextflow.io/docs/latest/config.html#scope-params
params {
    help = false
    outdir = "results"
    input = ''
    cohort_name = "cohort"
    ref = ''
    vep_species = ''
    vep_assembly = ''
    download_vep_cache = false
    multiqc_config = "${baseDir}/assets/multiqc_config.yml"
}

// Fail a task if any command returns non-zero exit code
// See https://www.nextflow.io/docs/latest/process.html#script
// See https://sydney-informatics-hub.github.io/tidbits/debugging-bash.html
shell = ['/bin/bash', '-euo', 'pipefail']

// Include base module configurations
includeConfig "config/modules.config"

profiles {
    singularity {
        singularity.enabled = true
    }
    gadi {
        includeConfig "config/gadi.config"
    }
}

// Produce a workflow diagram
dag {
    enabled = true
    overwrite = true
    file = "${params.outdir}/runInfo/parabricks-genomics001-dag.svg"
}

// Output resource and runtime reports for a workflow run
report {
    enabled = true
    overwrite = true
    file = "${params.outdir}/runInfo/parabricks-genomics001-report.html"
}

// Output an html timeline report
timeline {
    enabled = true
    overwrite = true
    file = "${params.outdir}/runInfo/parabricks-genomics001-timeline.html"
}

// Output process execution trace file
// See https://www.nextflow.io/docs/latest/tracing.html#trace-report
trace {
    enabled = true
    overwrite = true
    file = "${params.outdir}/runInfo/parabricks-genomics001-trace.txt"
}