cwl/lightning/fasta2numpy-wf.cwl

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 $namespaces:
   6   arv: "http://arvados.org/cwl#"
   7 cwlVersion: v1.2
   8 class: Workflow
   9 requirements:
  10   ScatterFeatureRequirement: {}
  11   SubworkflowFeatureRequirement: {}
  12   StepInputExpressionRequirement: {}
  13   MultipleInputFeatureRequirement: {}
  14
  15 inputs:
  16   tagset:
  17     type: File
  18   fastadirs:
  19     type:
  20       type: array
  21       items: Directory
  22   refdir:
  23     type: Directory
  24   batchsize:
  25     type: int
  26   regions:
  27     type: File?
  28   matchgenome:
  29     type: string
  30   threads:
  31     type: int
  32   mergeoutput:
  33     type: string
  34   expandregions:
  35     type: int
  36   phenotypesnofamilydir:
  37     type: Directory
  38   phenotypesdir:
  39     type: Directory
  40   trainingsetsize:
  41     type: float
  42   randomseed:
  43     type: int
  44   pcacomponents:
  45     type: int
  46   chrs: string[]
  47   snpeffdatadir: Directory
  48   genomeversion: string
  49   dbsnp:
  50     type: File
  51     secondaryFiles: [.csi]
  52   gnomaddir: Directory
  53   readmeinfo: string[]
  54
  55 outputs:
  56   stagednpydir:
  57     type: Directory
  58     outputSource: stage-output/stagednpydir
  59   stagedonehotnpydir:
  60     type: Directory
  61     outputSource: stage-output/stagedonehotnpydir
  62   stagedannotationdir:
  63     type: Directory
  64     outputSource: stage-output/stagedannotationdir
  65   readme:
  66     type: File
  67     outputSource: genreadme/readme
  68
  69 steps:
  70   batch-dirs:
  71     run: batch-dirs.cwl
  72     in:
  73       dirs: fastadirs
  74       batchsize: batchsize
  75     out: [batches]
  76
  77   lightning-import_data:
  78     run: lightning-import.cwl
  79     scatter: fastadirs
  80     in:
  81       saveincomplete:
  82         valueFrom: "false"
  83       tagset: tagset
  84       fastadirs: batch-dirs/batches
  85     out: [lib]
  86
  87   lightning-import_refs:
  88     run: lightning-import.cwl
  89     in:
  90       saveincomplete:
  91         valueFrom: "true"
  92       tagset: tagset
  93       fastadirs: refdir
  94     out: [lib]
  95
  96   lightning-slice:
  97     run: lightning-slice.cwl
  98     in:
  99       datalibs: lightning-import_data/lib
 100       reflib: lightning-import_refs/lib
 101     out: [libdir]
 102
 103   lightning-tiling-stats:
 104     run: lightning-tiling-stats.cwl
 105     in:
 106       libdir: lightning-slice/libdir
 107     out: [bed]
 108
 109   lightning-choose-samples:
 110     run: lightning-choose-samples.cwl
 111     in:
 112       matchgenome: matchgenome
 113       libdir: lightning-slice/libdir
 114       phenotypesdir: phenotypesnofamilydir
 115       trainingsetsize: trainingsetsize
 116       randomseed: randomseed
 117     out: [samplescsv]
 118
 119   lightning-slice-numpy:
 120     run: lightning-slice-numpy.cwl
 121     in:
 122       matchgenome: matchgenome
 123       libdir: lightning-slice/libdir
 124       regions: regions
 125       threads: threads
 126       mergeoutput: mergeoutput
 127       expandregions: expandregions
 128       samplescsv: lightning-choose-samples/samplescsv
 129     out: [outdir, npys, chunktagoffsetcsv]
 130
 131   lightning-slice-numpy-onehot:
 132     run: lightning-slice-numpy-onehot.cwl
 133     in:
 134       matchgenome: matchgenome
 135       libdir: lightning-slice/libdir
 136       regions: regions
 137       threads: threads
 138       mergeoutput: mergeoutput
 139       expandregions: expandregions
 140       samplescsv: lightning-choose-samples/samplescsv
 141     out: [outdir, npys]
 142
 143   lightning-slice-numpy-pca:
 144     run: lightning-slice-numpy-pca.cwl
 145     in:
 146       matchgenome: matchgenome
 147       libdir: lightning-slice/libdir
 148       regions: regions
 149       threads: threads
 150       mergeoutput: mergeoutput
 151       expandregions: expandregions
 152       samplescsv: lightning-choose-samples/samplescsv
 153       pcacomponents: pcacomponents
 154     out: [outdir, pcanpy, pcasamplescsv]
 155
 156   lightning-plot_1-2:
 157     run: lightning-plot.cwl
 158     in:
 159       pcanpy: lightning-slice-numpy-pca/pcanpy
 160       pcasamplescsv: lightning-slice-numpy-pca/pcasamplescsv
 161       phenotypesdir: phenotypesdir
 162       xcomponent:
 163         valueFrom: "1"
 164       ycomponent:
 165         valueFrom: "2"
 166     out: [png]
 167
 168   lightning-plot_2-3:
 169     run: lightning-plot.cwl
 170     in:
 171       pcanpy: lightning-slice-numpy-pca/pcanpy
 172       pcasamplescsv: lightning-slice-numpy-pca/pcasamplescsv
 173       phenotypesdir: phenotypesdir
 174       xcomponent:
 175         valueFrom: "2"
 176       ycomponent:
 177         valueFrom: "3"
 178     out: [png]
 179
 180   lightning-anno2vcf-onehot:
 181     run: lightning-anno2vcf.cwl
 182     in:
 183       annodir: lightning-slice-numpy-onehot/outdir
 184     out: [vcfdir]
 185
 186   make-libname:
 187     run: make-libname.cwl
 188     in:
 189       matchgenome: matchgenome
 190       genomeversion: genomeversion
 191     out: [libname]
 192
 193   annotate-wf:
 194     run: ../annotation/annotate-wf.cwl
 195     in:
 196       sample: make-libname/libname
 197       chrs: chrs
 198       vcfdir: lightning-anno2vcf-onehot/vcfdir
 199       snpeffdatadir: snpeffdatadir
 200       genomeversion: genomeversion
 201       dbsnp: dbsnp
 202       gnomaddir: gnomaddir
 203     out: [annotatedvcf, summary]
 204
 205   stage-output:
 206     run: stage-output.cwl
 207     in:
 208       libname: make-libname/libname
 209       npyfiles:
 210         source: [lightning-slice-numpy/npys, lightning-slice-numpy/chunktagoffsetcsv]
 211         linkMerge: merge_flattened
 212       onehotnpyfiles: lightning-slice-numpy-onehot/npys
 213       pcapngs:
 214         source: [lightning-plot_1-2/png, lightning-plot_2-3/png]
 215         linkMerge: merge_flattened
 216       bed: lightning-tiling-stats/bed
 217       annotatedvcf: annotate-wf/annotatedvcf
 218       summary: annotate-wf/summary
 219     out: [stagednpydir, stagedonehotnpydir, stagedannotationdir]
 220
 221   genreadme:
 222     run: genreadme.cwl
 223     in:
 224       samplescsv: lightning-choose-samples/samplescsv
 225       readmeinfo: readmeinfo
 226     out: [readme]