1 # Copyright (C) The Lightning Authors. All rights reserved.
3 # SPDX-License-Identifier: AGPL-3.0
8 InlineJavascriptRequirement: {}
9 SubworkflowFeatureRequirement: {}
10 MultipleInputFeatureRequirement: {}
19 phenotypesdir: Directory
22 snpeffdatadir: Directory
26 secondaryFiles: [.csi]
33 outputSource: stage-output/stagednpydir
36 outputSource: stage-output/stagedonehotnpydir
39 outputSource: stage-output/stagedannotationdir
42 outputSource: genreadme/readme
45 lightning-tiling-stats:
46 run: lightning-tiling-stats.cwl
47 when: $(inputs.regions == null)
52 lightning-slice-numpy:
53 run: lightning-slice-numpy.cwl
55 matchgenome: matchgenome
59 mergeoutput: mergeoutput
60 expandregions: expandregions
61 out: [outdir, npys, samplescsv, chunktagoffsetcsv]
63 lightning-slice-numpy-onehot:
64 run: lightning-slice-numpy-onehot.cwl
66 matchgenome: matchgenome
70 mergeoutput: mergeoutput
71 expandregions: expandregions
72 phenotypesdir: phenotypesdir
73 out: [outdir, npys, samplescsv]
75 lightning-anno2vcf-onehot:
76 run: lightning-anno2vcf.cwl
78 annodir: lightning-slice-numpy-onehot/outdir
82 run: ../annotation/annotate-wf.cwl
86 vcfdir: lightning-anno2vcf-onehot/vcfdir
87 snpeffdatadir: snpeffdatadir
88 genomeversion: genomeversion
91 out: [annotatedvcf, summary]
98 source: [lightning-slice-numpy/npys, lightning-slice-numpy/samplescsv, lightning-slice-numpy/chunktagoffsetcsv]
99 linkMerge: merge_flattened
101 source: [lightning-slice-numpy-onehot/npys, lightning-slice-numpy-onehot/samplescsv]
102 linkMerge: merge_flattened
103 bed: lightning-tiling-stats/bed
104 annotatedvcf: annotate-wf/annotatedvcf
105 summary: annotate-wf/summary
106 out: [stagednpydir, stagedonehotnpydir, stagedannotationdir]
111 samplescsv: lightning-slice-numpy/samplescsv
112 readmeinfo: readmeinfo