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     format: edam:format_1930  # FASTQ
  23     type:
  24      - File
  25      - File[]
  26     inputBinding:
  27       prefix: "--readFilesIn"
  28       itemSeparator: ","
  29       position: 1
  30   # If paired-end reads (like Illumina), both 1 and 2 must be provided.
  31   ReverseReads:
  32     format: edam:format_1930  # FASTQ
  33     type:
  34      - "null"
  35      - File
  36      - File[]
  37     inputBinding:
  38       prefix: ""
  39       separate: false
  40       itemSeparator: ","
  41       position: 2
  42
  43   # Optional Inputs
  44   Gtf:
  45     type: File?
  46     inputBinding:
  47       prefix: "--sjdbGTFfile"
  48
  49   Overhang:
  50     type: int?
  51     inputBinding:
  52       prefix: "--sjdbOverhang"
  53
  54   OutFilterType:
  55     type:
  56      - "null"
  57      - type: enum
  58        symbols:
  59         - Normal
  60         - BySJout
  61     inputBinding:
  62       prefix: "--outFilterType"
  63
  64   OutFilterIntronMotifs:
  65     type:
  66      - "null"
  67      - type: enum
  68        symbols:
  69         - None
  70         - RemoveNoncanonical
  71         - RemoveNoncanonicalUnannotated
  72     inputBinding:
  73       prefix: "--outFilterIntronMotifs"
  74
  75   OutSAMtype:
  76     type:
  77      - "null"
  78      - type: enum
  79        symbols:
  80         - "BAM"
  81         - "SAM"
  82     inputBinding:
  83       prefix: "--outSAMtype"
  84       position: 3
  85
  86   Unsorted:
  87     type: boolean?
  88     inputBinding:
  89       prefix: "Unsorted"
  90       position: 4
  91
  92   SortedByCoordinate:
  93     type: boolean?
  94     inputBinding:
  95       prefix: "SortedByCoordinate"
  96       position: 5
  97
  98   ReadFilesCommand:
  99     type: string?
 100     inputBinding:
 101       prefix: "--readFilesCommand"
 102
 103   AlignIntronMin:
 104     type: int?
 105     inputBinding:
 106       prefix: "--alignIntronMin"
 107
 108   AlignIntronMax:
 109     type: int?
 110     inputBinding:
 111       prefix: "--alignIntronMax"
 112
 113   AlignMatesGapMax:
 114     type: int?
 115     inputBinding:
 116       prefix: "--alignMatesGapMax"
 117
 118   AlignSJoverhangMin:
 119     type: int?
 120     inputBinding:
 121       prefix: "--alignSJoverhangMin"
 122
 123   AlignSJDBoverhangMin:
 124     type: int?
 125     inputBinding:
 126       prefix: "--alignSJDBoverhangMin"
 127
 128   SeedSearchStartLmax:
 129     type: int?
 130     inputBinding:
 131       prefix: "--seedSearchStartLmax"
 132
 133   ChimOutType:
 134     type:
 135      - "null"
 136      - type: enum
 137        symbols:
 138         - Junctions
 139         - SeparateSAMold
 140         - WithinBAM
 141         - "WithinBAM HardClip"
 142         - "WithinBAM SoftClip"
 143
 144   ChimSegmentMin:
 145     type: int?
 146     inputBinding:
 147       prefix: "--chimSegmentMin"
 148
 149   ChimJunctionOverhangMin:
 150     type: int?
 151     inputBinding:
 152       prefix: "--chimJunctionOverhangMin"
 153
 154   OutFilterMultimapNmax:
 155     type: int?
 156     inputBinding:
 157       prefix: "--outFilterMultimapNmax"
 158
 159   OutFilterMismatchNmax:
 160     type: int?
 161     inputBinding:
 162       prefix: "--outFilterMismatchNmax"
 163
 164   OutFilterMismatchNoverLmax:
 165     type: double?
 166     inputBinding:
 167       prefix: "--outFilterMismatchNoverLmax"
 168
 169   OutReadsUnmapped:
 170     type:
 171      - "null"
 172      - type: enum
 173        symbols:
 174         - None
 175         - Fastx
 176     inputBinding:
 177       prefix: "--outReadsUnmapped"
 178
 179   OutSAMstrandField:
 180     type:
 181      - "null"
 182      - type: enum
 183        symbols:
 184         - None
 185         - intronMotif
 186     inputBinding:
 187       prefix: "--outSAMstrandField"
 188
 189   OutSAMunmapped:
 190     type:
 191      - "null"
 192      - type: enum
 193        symbols:
 194         - None
 195         - Within
 196         - "Within KeepPairs"
 197     inputBinding:
 198       prefix: "--outSAMunmapped"
 199
 200   OutSAMmapqUnique:
 201     type: int?
 202     inputBinding:
 203       prefix: "--outSAMmapqUnique"
 204
 205   OutSamMode:
 206     type:
 207      - "null"
 208      - type: enum
 209        symbols:
 210         - None
 211         - Full
 212         - NoQS
 213     inputBinding:
 214       prefix: "--outSAMmode"
 215
 216   LimitOutSAMoneReadBytes:
 217     type: int?
 218     inputBinding:
 219       prefix: "--limitOutSAMoneReadBytes"
 220
 221   OutFileNamePrefix:
 222     type: string?
 223     inputBinding:
 224       prefix: "--outFileNamePrefix"
 225
 226   GenomeLoad:
 227     type:
 228      - "null"
 229      - type: enum
 230        symbols:
 231         - LoadAndKeep
 232         - LoadAndRemove
 233         - LoadAndExit
 234         - Remove
 235         - NoSharedMemory
 236     inputBinding:
 237       prefix: "--genomeLoad"
 238
 239 baseCommand: [STAR, --runMode, alignReads]
 240
 241 outputs:
 242   alignment:
 243     type:
 244      - File
 245     outputBinding:
 246       glob: "*.bam"
 247   unmapped_reads:
 248     type: ["null", File]
 249     outputBinding:
 250       glob: "Unmapped.out*"
 251
 252 $namespaces:
 253   edam: https://edamontology.org/
 254 $schemas:
 255   - https://edamontology.org/EDAM_1.18.owl