RNA-Seq/cwl/helper/STAR-Align.cwl

   1 #!/usr/bin/env cwl-runner
   2 cwlVersion: v1.0
   3 class: CommandLineTool
   4
   5 hints:
   6   DockerRequirement:
   7     dockerPull: "quay.io/biocontainers/star:2.7.5c--0"
   8
   9 inputs:
  10   # Required Inputs
  11   RunThreadN:
  12     type: int
  13     inputBinding:
  14       prefix: "--runThreadN"
  15
  16   GenomeDir:
  17     type: Directory
  18     inputBinding:
  19       prefix: "--genomeDir"
  20
  21   ForwardReads:
  22     type:
  23      - File
  24      - File[]
  25     inputBinding:
  26       prefix: "--readFilesIn"
  27       itemSeparator: ","
  28       position: 1
  29   # If paired-end reads (like Illumina), both 1 and 2 must be provided.
  30   ReverseReads:
  31     type:
  32      - "null"
  33      - File
  34      - File[]
  35     inputBinding:
  36       prefix: ""
  37       separate: false
  38       itemSeparator: ","
  39       position: 2
  40
  41   # Optional Inputs
  42   Gtf:
  43     type: File?
  44     inputBinding:
  45       prefix: "--sjdbGTFfile"
  46
  47   Overhang:
  48     type: int?
  49     inputBinding:
  50       prefix: "--sjdbOverhang"
  51
  52   OutFilterType:
  53     type:
  54      - "null"
  55      - type: enum
  56        symbols:
  57         - Normal
  58         - BySJout
  59     inputBinding:
  60       prefix: "--outFilterType"
  61
  62   OutFilterIntronMotifs:
  63     type:
  64      - "null"
  65      - type: enum
  66        symbols:
  67         - None
  68         - RemoveNoncanonical
  69         - RemoveNoncanonicalUnannotated
  70     inputBinding:
  71       prefix: "--outFilterIntronMotifs"
  72
  73   OutSAMtype:
  74     type:
  75      - "null"
  76      - type: enum
  77        symbols:
  78         - "BAM"
  79         - "SAM"
  80     inputBinding:
  81       prefix: "--outSAMtype"
  82       position: 3
  83
  84   Unsorted:
  85     type: boolean?
  86     inputBinding:
  87       prefix: "Unsorted"
  88       position: 4
  89
  90   SortedByCoordinate:
  91     type: boolean?
  92     inputBinding:
  93       prefix: "SortedByCoordinate"
  94       position: 5
  95
  96   ReadFilesCommand:
  97     type: string?
  98     inputBinding:
  99       prefix: "--readFilesCommand"
 100
 101   AlignIntronMin:
 102     type: int?
 103     inputBinding:
 104       prefix: "--alignIntronMin"
 105
 106   AlignIntronMax:
 107     type: int?
 108     inputBinding:
 109       prefix: "--alignIntronMax"
 110
 111   AlignMatesGapMax:
 112     type: int?
 113     inputBinding:
 114       prefix: "--alignMatesGapMax"
 115
 116   AlignSJoverhangMin:
 117     type: int?
 118     inputBinding:
 119       prefix: "--alignSJoverhangMin"
 120
 121   AlignSJDBoverhangMin:
 122     type: int?
 123     inputBinding:
 124       prefix: "--alignSJDBoverhangMin"
 125
 126   SeedSearchStartLmax:
 127     type: int?
 128     inputBinding:
 129       prefix: "--seedSearchStartLmax"
 130
 131   ChimOutType:
 132     type:
 133      - "null"
 134      - type: enum
 135        symbols:
 136         - Junctions
 137         - SeparateSAMold
 138         - WithinBAM
 139         - "WithinBAM HardClip"
 140         - "WithinBAM SoftClip"
 141
 142   ChimSegmentMin:
 143     type: int?
 144     inputBinding:
 145       prefix: "--chimSegmentMin"
 146
 147   ChimJunctionOverhangMin:
 148     type: int?
 149     inputBinding:
 150       prefix: "--chimJunctionOverhangMin"
 151
 152   OutFilterMultimapNmax:
 153     type: int?
 154     inputBinding:
 155       prefix: "--outFilterMultimapNmax"
 156
 157   OutFilterMismatchNmax:
 158     type: int?
 159     inputBinding:
 160       prefix: "--outFilterMismatchNmax"
 161
 162   OutFilterMismatchNoverLmax:
 163     type: double?
 164     inputBinding:
 165       prefix: "--outFilterMismatchNoverLmax"
 166
 167   OutReadsUnmapped:
 168     type:
 169      - "null"
 170      - type: enum
 171        symbols:
 172         - None
 173         - Fastx
 174     inputBinding:
 175       prefix: "--outReadsUnmapped"
 176
 177   OutSAMstrandField:
 178     type:
 179      - "null"
 180      - type: enum
 181        symbols:
 182         - None
 183         - intronMotif
 184     inputBinding:
 185       prefix: "--outSAMstrandField"
 186
 187   OutSAMunmapped:
 188     type:
 189      - "null"
 190      - type: enum
 191        symbols:
 192         - None
 193         - Within
 194         - "Within KeepPairs"
 195     inputBinding:
 196       prefix: "--outSAMunmapped"
 197
 198   OutSAMmapqUnique:
 199     type: int?
 200     inputBinding:
 201       prefix: "--outSAMmapqUnique"
 202
 203   OutSamMode:
 204     type:
 205      - "null"
 206      - type: enum
 207        symbols:
 208         - None
 209         - Full
 210         - NoQS
 211     inputBinding:
 212       prefix: "--outSAMmode"
 213
 214   LimitOutSAMoneReadBytes:
 215     type: int?
 216     inputBinding:
 217       prefix: "--limitOutSAMoneReadBytes"
 218
 219   OutFileNamePrefix:
 220     type: string?
 221     inputBinding:
 222       prefix: "--outFileNamePrefix"
 223
 224   GenomeLoad:
 225     type:
 226      - "null"
 227      - type: enum
 228        symbols:
 229         - LoadAndKeep
 230         - LoadAndRemove
 231         - LoadAndExit
 232         - Remove
 233         - NoSharedMemory
 234     inputBinding:
 235       prefix: "--genomeLoad"
 236
 237 baseCommand: [STAR, --runMode, alignReads]
 238
 239 outputs:
 240   alignment:
 241     type:
 242      - File
 243     outputBinding:
 244       glob: "*.bam"
 245   unmapped_reads:
 246     type: ["null", File]
 247     outputBinding:
 248       glob: "Unmapped.out*"