cwl/lightning/lightning-slice-numpy-anno2vcf-wf.cwl

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 cwlVersion: v1.2
   6 class: Workflow
   7 requirements:
   8   InlineJavascriptRequirement: {}
   9   SubworkflowFeatureRequirement: {}
  10   MultipleInputFeatureRequirement: {}
  11
  12 inputs:
  13   matchgenome: string
  14   libdir: Directory
  15   regions: File?
  16   threads: int
  17   mergeoutput: string
  18   expandregions: int
  19   phenotypesdir: Directory
  20   libname: string
  21   chrs: string[]
  22   snpeffdatadir: Directory
  23   genomeversion: string
  24   dbsnp:
  25     type: File
  26     secondaryFiles: [.csi]
  27   gnomaddir: Directory
  28   readmeinfo: string[]
  29
  30 outputs:
  31   stagednpydir:
  32     type: Directory
  33     outputSource: stage-output/stagednpydir
  34   stagedonehotnpydir:
  35     type: Directory
  36     outputSource: stage-output/stagedonehotnpydir
  37   stagedannotationdir:
  38     type: Directory?
  39     outputSource: stage-output/stagedannotationdir
  40   readme:
  41     type: File
  42     outputSource: genreadme/readme
  43
  44 steps:
  45   lightning-tiling-stats:
  46     run: lightning-tiling-stats.cwl
  47     when: $(inputs.regions == null)
  48     in:
  49       libdir: libdir
  50     out: [bed]
  51
  52   lightning-slice-numpy:
  53     run: lightning-slice-numpy.cwl
  54     in:
  55       matchgenome: matchgenome
  56       libdir: libdir
  57       regions: regions
  58       threads: threads
  59       mergeoutput: mergeoutput
  60       expandregions: expandregions
  61     out: [outdir, npys, samplescsv, chunktagoffsetcsv]
  62
  63   lightning-slice-numpy-onehot:
  64     run: lightning-slice-numpy-onehot.cwl
  65     in:
  66       matchgenome: matchgenome
  67       libdir: libdir
  68       regions: regions
  69       threads: threads
  70       mergeoutput: mergeoutput
  71       expandregions: expandregions
  72       phenotypesdir: phenotypesdir
  73     out: [outdir, npys, samplescsv]
  74
  75   lightning-anno2vcf-onehot:
  76     run: lightning-anno2vcf.cwl
  77     in:
  78       annodir: lightning-slice-numpy-onehot/outdir
  79     out: [vcfdir]
  80
  81   annotate-wf:
  82     run: ../annotation/annotate-wf.cwl
  83     in:
  84       sample: libname
  85       chrs: chrs
  86       vcfdir: lightning-anno2vcf-onehot/vcfdir
  87       snpeffdatadir: snpeffdatadir
  88       genomeversion: genomeversion
  89       dbsnp: dbsnp
  90       gnomaddir: gnomaddir
  91     out: [annotatedvcf, summary]
  92
  93   stage-output:
  94     run: stage-output.cwl
  95     in:
  96       libname: libname
  97       npyfiles:
  98         source: [lightning-slice-numpy/npys, lightning-slice-numpy/samplescsv, lightning-slice-numpy/chunktagoffsetcsv]
  99         linkMerge: merge_flattened
 100       onehotnpyfiles:
 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]
 107
 108   genreadme:
 109     run: genreadme.cwl
 110     in:
 111       samplescsv: lightning-slice-numpy/samplescsv
 112       readmeinfo: readmeinfo
 113     out: [readme]