cwl/lightning/imputation-gvcf2fasta-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
  14 inputs:
  15   sampleids:
  16     type: string[]
  17   splitvcfdirs:
  18     type: Directory[]
  19   gqcutoff:
  20     type: int
  21   genomebed:
  22     type: File
  23   ref:
  24     type: File
  25   chrs: string[]
  26   refsdir: Directory
  27   mapsdir: Directory
  28   panelnocallbed: File
  29   panelcallbed: File
  30   tagset:
  31     type: File
  32   refdir:
  33     type: Directory
  34   batchsize:
  35     type: int
  36   regions:
  37     type: File?
  38   matchgenome:
  39     type: string
  40   threads:
  41     type: int
  42   mergeoutput:
  43     type: string
  44   expandregions:
  45     type: int
  46
  47 outputs: []
  48
  49 steps:
  50   scatter-gvcf2fasta_splitvcf-imputation-wf:
  51     run: ../gvcf2fasta/scatter-gvcf2fasta_splitvcf-imputation-wf.cwl
  52     in:
  53       sampleids: sampleids
  54       splitvcfdirs: splitvcfdirs
  55       gqcutoff: gqcutoff
  56       genomebed: genomebed
  57       ref: ref
  58       chrs: chrs
  59       refsdir: refsdir
  60       mapsdir: mapsdir
  61       panelnocallbed: panelnocallbed
  62       panelcallbed: panelcallbed
  63     out: [fas]
  64
  65   make-fastadirs:
  66     run: make-fastadirs.cwl
  67     in:
  68       fas: scatter-gvcf2fasta_splitvcf-imputation-wf/fas
  69     out: [fastadirs]
  70
  71   batch-dirs:
  72     run: batch-dirs.cwl
  73     in:
  74       dirs: make-fastadirs/fastadirs
  75       batchsize: batchsize
  76     out: [batches]
  77
  78   lightning-import_data:
  79     run: lightning-import.cwl
  80     scatter: fastadirs
  81     in:
  82       saveincomplete:
  83         valueFrom: "false"
  84       tagset: tagset
  85       fastadirs: batch-dirs/batches
  86     out: [lib]
  87
  88   lightning-import_refs:
  89     run: lightning-import.cwl
  90     in:
  91       saveincomplete:
  92         valueFrom: "true"
  93       tagset: tagset
  94       fastadirs: refdir
  95     out: [lib]
  96
  97   lightning-slice:
  98     run: lightning-slice.cwl
  99     in:
 100       datalibs: lightning-import_data/lib
 101       reflib: lightning-import_refs/lib
 102     out: [libdir]
 103
 104   lightning-tiling-stats:
 105     run: lightning-tiling-stats.cwl
 106     in:
 107       libdir: lightning-slice/libdir
 108     out: [bed]
 109
 110   lightning-slice-numpy:
 111     run: lightning-slice-numpy.cwl
 112     in:
 113       matchgenome: matchgenome
 114       libdir: lightning-slice/libdir
 115       regions: regions
 116       threads: threads
 117       mergeoutput: mergeoutput
 118       expandregions: expandregions
 119     out: [outdir, npys, chunktagoffsetcsv]