cwl/lightning/fasta2numpy-test-release-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: false
  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   readme:
  60     type: File
  61     outputSource: genreadme/readme
  62
  63 steps:
  64   batch-dirs:
  65     run: batch-dirs.cwl
  66     in:
  67       dirs: fastadirs
  68       batchsize: batchsize
  69     out: [batches]
  70
  71   lightning-import_data:
  72     run: lightning-import.cwl
  73     scatter: fastadirs
  74     in:
  75       saveincomplete:
  76         valueFrom: "false"
  77       tagset: tagset
  78       fastadirs: batch-dirs/batches
  79     out: [lib]
  80
  81   lightning-import_refs:
  82     run: lightning-import.cwl
  83     in:
  84       saveincomplete:
  85         valueFrom: "true"
  86       tagset: tagset
  87       fastadirs: refdir
  88     out: [lib]
  89
  90   lightning-slice:
  91     run: lightning-slice.cwl
  92     in:
  93       datalibs: lightning-import_data/lib
  94       reflib: lightning-import_refs/lib
  95     out: [libdir]
  96
  97   lightning-tiling-stats:
  98     run: lightning-tiling-stats.cwl
  99     in:
 100       libdir: lightning-slice/libdir
 101     out: [bed]
 102
 103   lightning-choose-samples:
 104     run: lightning-choose-samples.cwl
 105     in:
 106       matchgenome: matchgenome
 107       libdir: lightning-slice/libdir
 108       phenotypesdir: phenotypesnofamilydir
 109       trainingsetsize: trainingsetsize
 110       randomseed: randomseed
 111     out: [samplescsv]
 112
 113   lightning-slice-numpy-pca:
 114     run: lightning-slice-numpy-pca.cwl
 115     in:
 116       matchgenome: matchgenome
 117       libdir: lightning-slice/libdir
 118       regions: regions
 119       threads: threads
 120       mergeoutput: mergeoutput
 121       expandregions: expandregions
 122       samplescsv: lightning-choose-samples/samplescsv
 123       pcacomponents: pcacomponents
 124     out: [outdir, pcanpy, pcasamplescsv]
 125
 126   lightning-slice-numpy:
 127     run: lightning-slice-numpy-onehot.cwl
 128     in:
 129       matchgenome: matchgenome
 130       libdir: lightning-slice/libdir
 131       regions: regions
 132       mergeoutput: mergeoutput
 133       expandregions: expandregions
 134       samplescsv: lightning-slice-numpy-pca/pcasamplescsv
 135     out: [outdir, npys]
 136
 137   lightning-plot_1-2:
 138     run: lightning-plot.cwl
 139     in:
 140       pcanpy: lightning-slice-numpy-pca/pcanpy
 141       pcasamplescsv: lightning-slice-numpy-pca/pcasamplescsv
 142       phenotypesdir: phenotypesdir
 143       xcomponent:
 144         valueFrom: "1"
 145       ycomponent:
 146         valueFrom: "2"
 147     out: [png]
 148
 149   lightning-plot_2-3:
 150     run: lightning-plot.cwl
 151     in:
 152       pcanpy: lightning-slice-numpy-pca/pcanpy
 153       pcasamplescsv: lightning-slice-numpy-pca/pcasamplescsv
 154       phenotypesdir: phenotypesdir
 155       xcomponent:
 156         valueFrom: "2"
 157       ycomponent:
 158         valueFrom: "3"
 159     out: [png]
 160
 161   lightning-anno2vcf-onehot:
 162     run: lightning-anno2vcf.cwl
 163     in:
 164       annodir: lightning-slice-numpy/outdir
 165     out: [vcfdir]
 166
 167   make-libname:
 168     run: make-libname.cwl
 169     in:
 170       matchgenome: matchgenome
 171       genomeversion: genomeversion
 172     out: [libname]
 173
 174   annotate-wf:
 175     run: ../annotation/annotate-wf.cwl
 176     in:
 177       sample: make-libname/libname
 178       chrs: chrs
 179       vcfdir: lightning-anno2vcf-onehot/vcfdir
 180       snpeffdatadir: snpeffdatadir
 181       genomeversion: genomeversion
 182       dbsnp: dbsnp
 183       gnomaddir: gnomaddir
 184     out: [annotatedvcf, summary]
 185
 186   genreadme:
 187     run: genreadme.cwl
 188     in:
 189       samplescsv: lightning-choose-samples/samplescsv
 190       readmeinfo: readmeinfo
 191     out: [readme]