alea-createGenome_new.cwl

cwlVersion: v1.0

class: CommandLineTool

baseCommand: ["alea", "createGenome"]

requirements:
- $import: alea-docker.yml
- $import: envvar-global.yml
- class: InlineJavascriptRequirement
- class: EnvVarRequirement
  envDef:
  - envName: "HOME"
    envValue: $(runtime.outdir)
  - envName: "AL_USE_CONCATENATED_GENOME"
    envValue: $(inputs.CONCATENATED_GENOME?"1":"0")
  - envName: "AL_BWA_ALN_PARAMS"
    envValue: "-k 0 -n 0 -t 4"
  - envName: "AL_DIR_TOOLS"
    envValue: "/usr/local/bin/"

inputs:
 reference:
  type: File
  doc: |
    the reference genome fasta file
  inputBinding:
    position: 2
  secondaryFiles:
  - '.fai'

 phased:
  type: File
  doc: |
    the phased variants vcf file (including SNPs and Indels)
    or the phased SNPs (should be specified first)
  inputBinding:
    position: 3
  secondaryFiles:
  - '.tbi'

 phasedindels:
  type: File?
  doc: |
    the phased Indels (should be specified second)
  inputBinding:
    position: 4
  secondaryFiles:
  - '.tbi'

 strain1:
  type: string
  doc: |
    name of strain1 exactly as specified in the vcf file (e.g. hap1)
    mouse:
        129P2_OlaHsd  (129P2/OlaHsd)  F 52
        129S1_SvImJ (129S1/SvImJ) F 68
        129S5SvEvBrd  (129S5SvEvBrd)  F 22
        A_J (A/J) F 52
        AKR_J (AKR/J) F 57
        BALB_cJ (BALB/cJ) F 62
        BTBR_T+_Itpr3tf_J (BTBR T+ Itpr3tf/J) M 85
        BUB_BnJ (BUB/BnJ) M 49
        C3H_HeH (C3H/HeH) F 14
        C3H_HeJ (C3H/HeJ) F 63
        C57BL_10J (C57BL/10J) M 37
        C57BL_6NJ (C57BL/6NJ) F 61
        C57BR_cdJ (C57BR/cdJ) M 51
        C57L_J  (C57L/J)  M 64
        C58_J (C58/J) M 55
        CAST_EiJ  (CAST/EiJ)  F 53
        CBA_J (CBA/J) F 56
        DBA_1J  (DBA/1J)  M 49
        DBA_2J  (DBA/2J)  F 56
        FVB_NJ  (FVB/NJ)  F 73
        I_LnJ (I/LnJ) M 45
        KK_HiJ  (KK/HiJ)  M 55
        LEWES_EiJ (LEWES/EiJ) F 19
        LP_J  (LP/J)  F 54
        MOLF_EiJ  (MOLF/EiJ)  M 40
        NOD_ShiLtJ  (NOD/ShiLtJ)  F 66
        NZB_B1NJ  (NZB/B1NJ)  M 47
        NZO_HlLtJ (NZO/HlLtJ) F 72
        NZW_LacJ  (NZW/LacJ)  M 58
        PWK_PhJ (PWK/PhJ) F 53
        RF_J  (RF/J)  M 54
        SEA_GnJ (SEA/GnJ) M 49
        SPRET_EiJ (SPRET/EiJ) F 67
        ST_bJ (ST/bJ) M 81
        WSB_EiJ (WSB/EiJ) F 51
        ZALENDE_EiJ (ZALENDE/EiJ) M 19
  inputBinding:
    position: 5

 strain2:
  type: string
  doc: |
    name of strain2 exactly as specified in the vcf file (e.g. hap2)
  inputBinding:
    position: 6

 outputDir:
  type: string
  doc: |
    location of the output directory
  inputBinding:
    position: 7

 CONCATENATED_GENOME:
  type: boolean
  default: false

outputs: 
  strain1_indices:
    type: File
    outputBinding:
      glob: $(inputs.outputDir+"/"+inputs.strain1+".fasta")
    secondaryFiles:
    - ".amb"
    - ".ann"
    - ".bwt"
    - ".fai"
    - ".pac"
    - ".refmap"
    - ".sa"

  strain2_indices:
    type: File
    outputBinding:
      glob: $(inputs.outputDir+"/"+inputs.strain1+".fasta")
    secondaryFiles:
    - ".amb"
    - ".ann"
    - ".bwt"
    - ".fai"
    - ".pac"
    - ".refmap"
    - ".sa"

arguments:
  - valueFrom: $(inputs.phasedindels?"-snps-indels-separately":[])
    position: 1

$namespaces:
  s: http://schema.org/