1 # Copyright (C) The Lightning Authors. All rights reserved.
3 # SPDX-License-Identifier: AGPL-3.0
8 ScatterFeatureRequirement: {}
14 snpeffdatadir: Directory
18 secondaryFiles: [.csi]
24 secondaryFiles: [.tbi]
25 outputSource: bcftools-concat/vcf
28 outputSource: totalcounts/summary
38 out: [samples, vcfs, gnomads]
42 scatter: [sample, vcf]
43 scatterMethod: dotproduct
45 sample: getfiles/samples
49 snpeff-bcftools-annotate:
50 run: snpeff-bcftools-annotate.cwl
51 scatter: [sample, vcf, gnomad]
52 scatterMethod: dotproduct
54 vcf: preprocess/trimmedvcf
55 sample: getfiles/samples
56 snpeffdatadir: snpeffdatadir
57 genomeversion: genomeversion
59 gnomad: getfiles/gnomads
63 run: bcftools-concat.cwl
66 vcfs: snpeff-bcftools-annotate/annotatedvcf
71 scatter: [sample, vcf]
72 scatterMethod: dotproduct
74 sample: getfiles/samples
75 vcf: snpeff-bcftools-annotate/annotatedvcf
82 counts: getcount/count