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 hints:
  15   arv:UsePreemptible:
  16     usePreemptible: true
  17
  18 inputs:
  19   tagset:
  20     type: File
  21   fastadirs:
  22     type:
  23       type: array
  24       items: Directory
  25   refdir:
  26     type: Directory
  27   batchsize:
  28     type: int
  29   regions:
  30     type: File?
  31   matchgenome:
  32     type: string
  33   threads:
  34     type: int
  35   mergeoutput:
  36     type: string
  37   expandregions:
  38     type: int
  39   phenotypesnofamilydir:
  40     type: Directory
  41   phenotypesdir:
  42     type: Directory
  43   trainingsetsize:
  44     type: float
  45   randomseed:
  46     type: int
  47   pcacomponents:
  48     type: int
  49   chrs: string[]
  50   snpeffdatadir: Directory
  51   genomeversion: string
  52   dbsnp:
  53     type: File
  54     secondaryFiles: [.csi]
  55   gnomaddir: Directory
  56   readmeinfo: string[]
  57
  58 outputs: []
  59 #  stagednpydir:
  60 #    type: Directory
  61 #    outputSource: stage-output/stagednpydir
  62 #  stagedonehotnpydir:
  63 #    type: Directory
  64 #    outputSource: stage-output/stagedonehotnpydir
  65 #  stagedannotationdir:
  66 #    type: Directory
  67 #    outputSource: stage-output/stagedannotationdir
  68 #  readme:
  69 #    type: File
  70 #    outputSource: genreadme/readme
  71
  72 steps:
  73   batch-dirs:
  74     run: batch-dirs.cwl
  75     in:
  76       dirs: fastadirs
  77       batchsize: batchsize
  78     out: [batches]
  79
  80   lightning-import_data:
  81     run: lightning-import.cwl
  82     scatter: fastadirs
  83     in:
  84       saveincomplete:
  85         valueFrom: "false"
  86       tagset: tagset
  87       fastadirs: batch-dirs/batches
  88     out: [lib]
  89
  90   lightning-import_refs:
  91     run: lightning-import.cwl
  92     in:
  93       saveincomplete:
  94         valueFrom: "true"
  95       tagset: tagset
  96       fastadirs: refdir
  97     out: [lib]
  98
  99   lightning-slice:
 100     run: lightning-slice.cwl
 101     in:
 102       datalibs: lightning-import_data/lib
 103       reflib: lightning-import_refs/lib
 104     out: [libdir]
 105
 106   lightning-tiling-stats:
 107     run: lightning-tiling-stats.cwl
 108     in:
 109       libdir: lightning-slice/libdir
 110     out: [bed]
 111
 112   lightning-choose-samples:
 113     run: lightning-choose-samples.cwl
 114     in:
 115       matchgenome: matchgenome
 116       libdir: lightning-slice/libdir
 117       phenotypesdir: phenotypesnofamilydir
 118       trainingsetsize: trainingsetsize
 119       randomseed: randomseed
 120     out: [samplescsv]
 121
 122 #  lightning-slice-numpy:
 123 #    run: lightning-slice-numpy.cwl
 124 #    in:
 125 #      matchgenome: matchgenome
 126 #      libdir: lightning-slice/libdir
 127 #      regions: regions
 128 #      threads: threads
 129 #      mergeoutput: mergeoutput
 130 #      expandregions: expandregions
 131 #      samplescsv: lightning-choose-samples/samplescsv
 132 #    out: [outdir, npys, chunktagoffsetcsv]
 133
 134   lightning-slice-numpy-onehot_chi2:
 135     run: lightning-slice-numpy-onehot.cwl
 136     in:
 137       matchgenome: matchgenome
 138       libdir: lightning-slice/libdir
 139       regions: regions
 140       mergeoutput: mergeoutput
 141       expandregions: expandregions
 142       samplescsv: lightning-choose-samples/samplescsv
 143     out: [outdir, npys]
 144
 145   lightning-slice-numpy-onehot_logisticregression:
 146     run: lightning-slice-numpy-onehot.cwl
 147     in:
 148       matchgenome: matchgenome
 149       libdir: lightning-slice/libdir
 150       regions: regions
 151       mergeoutput: mergeoutput
 152       expandregions: expandregions
 153       samplescsv: lightning-slice-numpy-pca/pcasamplescsv
 154     out: [outdir, npys]
 155
 156   lightning-slice-numpy-pca:
 157     run: lightning-slice-numpy-pca.cwl
 158     in:
 159       matchgenome: matchgenome
 160       libdir: lightning-slice/libdir
 161       regions: regions
 162       threads: threads
 163       mergeoutput: mergeoutput
 164       expandregions: expandregions
 165       samplescsv: lightning-choose-samples/samplescsv
 166       pcacomponents: pcacomponents
 167     out: [outdir, pcanpy, pcasamplescsv]
 168
 169   lightning-plot_1-2:
 170     run: lightning-plot.cwl
 171     in:
 172       pcanpy: lightning-slice-numpy-pca/pcanpy
 173       pcasamplescsv: lightning-slice-numpy-pca/pcasamplescsv
 174       phenotypesdir: phenotypesdir
 175       xcomponent:
 176         valueFrom: "1"
 177       ycomponent:
 178         valueFrom: "2"
 179     out: [png]
 180
 181   lightning-plot_2-3:
 182     run: lightning-plot.cwl
 183     in:
 184       pcanpy: lightning-slice-numpy-pca/pcanpy
 185       pcasamplescsv: lightning-slice-numpy-pca/pcasamplescsv
 186       phenotypesdir: phenotypesdir
 187       xcomponent:
 188         valueFrom: "2"
 189       ycomponent:
 190         valueFrom: "3"
 191     out: [png]
 192
 193 #  lightning-anno2vcf-onehot:
 194 #    run: lightning-anno2vcf.cwl
 195 #    in:
 196 #      annodir: lightning-slice-numpy-onehot/outdir
 197 #    out: [vcfdir]
 198
 199 #  make-libname:
 200 #    run: make-libname.cwl
 201 #    in:
 202 #      matchgenome: matchgenome
 203 #      genomeversion: genomeversion
 204 #    out: [libname]
 205
 206 #  annotate-wf:
 207 #    run: ../annotation/annotate-wf.cwl
 208 #    in:
 209 #      sample: make-libname/libname
 210 #      chrs: chrs
 211 #      vcfdir: lightning-anno2vcf-onehot/vcfdir
 212 #      snpeffdatadir: snpeffdatadir
 213 #      genomeversion: genomeversion
 214 #      dbsnp: dbsnp
 215 #      gnomaddir: gnomaddir
 216 #    out: [annotatedvcf, summary]
 217
 218 #  stage-output:
 219 #    run: stage-output.cwl
 220 #    in:
 221 #      libname: make-libname/libname
 222 #      npyfiles:
 223 #        source: [lightning-slice-numpy/npys, lightning-slice-numpy/chunktagoffsetcsv]
 224 #        linkMerge: merge_flattened
 225 #      onehotnpyfiles: lightning-slice-numpy-onehot/npys
 226 #      pcapngs:
 227 #        source: [lightning-plot_1-2/png, lightning-plot_2-3/png]
 228 #        linkMerge: merge_flattened
 229 #      bed: lightning-tiling-stats/bed
 230 #      annotatedvcf: annotate-wf/annotatedvcf
 231 #      summary: annotate-wf/summary
 232 #    out: [stagednpydir, stagedonehotnpydir, stagedannotationdir]
 233
 234 #  genreadme:
 235 #    run: genreadme.cwl
 236 #    in:
 237 #      samplescsv: lightning-choose-samples/samplescsv
 238 #      readmeinfo: readmeinfo
 239 #    out: [readme]