cwl/lightning/libray2numpy-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 #hints:
  14 #  arv:IntermediateOutput:
  15 #    outputTTL: 604800
  16
  17 inputs:
  18   tagset:
  19     type: File
  20   fastadirs:
  21     type:
  22       type: array
  23       items: Directory
  24   refdirs:
  25     type:
  26       type: array
  27       items: Directory
  28   batchsize:
  29     type: int
  30   matchgenome_array:
  31     type: string[]
  32   regions_nestedarray:
  33     type:
  34       type: array
  35       items:
  36         type: array
  37         items: [File, "null"]
  38   threads_array:
  39     type: int[]
  40   mergeoutput_array:
  41     type: string[]
  42   expandregions_array:
  43     type: int[]
  44   phenotypesdir:
  45     type: Directory
  46   chrs: string[]
  47   snpeffdatadir: Directory
  48   genomeversion_array: 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: lightning-slice-numpy-anno2vcf-wf/stagednpydir
  59   stagedonehotnpydir:
  60     type: Directory[]
  61     outputSource: lightning-slice-numpy-anno2vcf-wf/stagedonehotnpydir
  62   stagedannotationdir:
  63     type:
  64       type: array
  65       items: [Directory, "null"]
  66     outputSource: lightning-slice-numpy-anno2vcf-wf/stagedannotationdir
  67   readme:
  68     type: File[]
  69     outputSource: lightning-slice-numpy-anno2vcf-wf/readme
  70
  71 steps:
  72   batch-dirs:
  73     run: batch-dirs.cwl
  74     in:
  75       dirs: fastadirs
  76       batchsize: batchsize
  77     out: [batches]
  78
  79   lightning-import_data:
  80     run: lightning-import.cwl
  81     scatter: fastadirs
  82     in:
  83       saveincomplete:
  84         valueFrom: "false"
  85       tagset: tagset
  86       fastadirs: batch-dirs/batches
  87     out: [lib]
  88
  89   lightning-import_refs:
  90     run: lightning-import.cwl
  91     scatter: fastadirs
  92     in:
  93       saveincomplete:
  94         valueFrom: "true"
  95       tagset: tagset
  96       fastadirs: refdirs
  97     out: [lib]
  98
  99   lightning-slice:
 100     run: lightning-slice.cwl
 101     scatter: reflib
 102     in:
 103       datalibs: lightning-import_data/lib
 104       reflib: lightning-import_refs/lib
 105     out: [libdir]
 106
 107   make-arrays:
 108     run: make-arrays.cwl
 109     in:
 110       matchgenome_array: matchgenome_array
 111       libdir_array: lightning-slice/libdir
 112       genomeversion_array: genomeversion_array
 113       regions_nestedarray: regions_nestedarray
 114       threads_array: threads_array
 115       mergeoutput_array: mergeoutput_array
 116       expandregions_array: expandregions_array
 117     out: [full_matchgenome_array, full_libdir_array, full_genomeversion_array, full_regions_array, full_threads_array, full_mergeoutput_array, full_expandregions_array, full_libname_array]
 118
 119   lightning-slice-numpy-anno2vcf-wf:
 120     run: lightning-slice-numpy-anno2vcf-wf.cwl
 121     scatter: [matchgenome, libdir, genomeversion, regions, threads, mergeoutput, expandregions, libname]
 122     scatterMethod: dotproduct
 123     in:
 124       matchgenome: make-arrays/full_matchgenome_array
 125       libdir: make-arrays/full_libdir_array
 126       regions: make-arrays/full_regions_array
 127       threads: make-arrays/full_threads_array
 128       mergeoutput: make-arrays/full_mergeoutput_array
 129       expandregions: make-arrays/full_expandregions_array
 130       phenotypesdir: phenotypesdir
 131       libname: make-arrays/full_libname_array
 132       chrs: chrs
 133       snpeffdatadir: snpeffdatadir
 134       genomeversion: make-arrays/full_genomeversion_array
 135       dbsnp: dbsnp
 136       gnomaddir: gnomaddir
 137       readmeinfo: readmeinfo
 138     out: [stagednpydir, stagedonehotnpydir, stagedannotationdir, readme]