--- /dev/null
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+hints:
+ DockerRequirement:
+ dockerPull: "quay.io/biocontainers/star:2.7.5c--0"
+
+inputs:
+ # Required Inputs
+ RunThreadN:
+ type: int
+ inputBinding:
+ prefix: "--runThreadN"
+
+ GenomeDir:
+ type: Directory
+ inputBinding:
+ prefix: "--genomeDir"
+
+ ForwardReads:
+ format: edam:format_1930 # FASTQ
+ type:
+ - File
+ - File[]
+ inputBinding:
+ prefix: "--readFilesIn"
+ itemSeparator: ","
+ position: 1
+ # If paired-end reads (like Illumina), both 1 and 2 must be provided.
+ ReverseReads:
+ format: edam:format_1930 # FASTQ
+ type:
+ - "null"
+ - File
+ - File[]
+ inputBinding:
+ prefix: ""
+ separate: false
+ itemSeparator: ","
+ position: 2
+
+ # Optional Inputs
+ Gtf:
+ type: File?
+ inputBinding:
+ prefix: "--sjdbGTFfile"
+
+ Overhang:
+ type: int?
+ inputBinding:
+ prefix: "--sjdbOverhang"
+
+ OutFilterType:
+ type:
+ - "null"
+ - type: enum
+ symbols:
+ - Normal
+ - BySJout
+ inputBinding:
+ prefix: "--outFilterType"
+
+ OutFilterIntronMotifs:
+ type:
+ - "null"
+ - type: enum
+ symbols:
+ - None
+ - RemoveNoncanonical
+ - RemoveNoncanonicalUnannotated
+ inputBinding:
+ prefix: "--outFilterIntronMotifs"
+
+ OutSAMtype:
+ type:
+ - "null"
+ - type: enum
+ symbols:
+ - "BAM"
+ - "SAM"
+ inputBinding:
+ prefix: "--outSAMtype"
+ position: 3
+
+ Unsorted:
+ type: boolean?
+ inputBinding:
+ prefix: "Unsorted"
+ position: 4
+
+ SortedByCoordinate:
+ type: boolean?
+ inputBinding:
+ prefix: "SortedByCoordinate"
+ position: 5
+
+ ReadFilesCommand:
+ type: string?
+ inputBinding:
+ prefix: "--readFilesCommand"
+
+ AlignIntronMin:
+ type: int?
+ inputBinding:
+ prefix: "--alignIntronMin"
+
+ AlignIntronMax:
+ type: int?
+ inputBinding:
+ prefix: "--alignIntronMax"
+
+ AlignMatesGapMax:
+ type: int?
+ inputBinding:
+ prefix: "--alignMatesGapMax"
+
+ AlignSJoverhangMin:
+ type: int?
+ inputBinding:
+ prefix: "--alignSJoverhangMin"
+
+ AlignSJDBoverhangMin:
+ type: int?
+ inputBinding:
+ prefix: "--alignSJDBoverhangMin"
+
+ SeedSearchStartLmax:
+ type: int?
+ inputBinding:
+ prefix: "--seedSearchStartLmax"
+
+ ChimOutType:
+ type:
+ - "null"
+ - type: enum
+ symbols:
+ - Junctions
+ - SeparateSAMold
+ - WithinBAM
+ - "WithinBAM HardClip"
+ - "WithinBAM SoftClip"
+
+ ChimSegmentMin:
+ type: int?
+ inputBinding:
+ prefix: "--chimSegmentMin"
+
+ ChimJunctionOverhangMin:
+ type: int?
+ inputBinding:
+ prefix: "--chimJunctionOverhangMin"
+
+ OutFilterMultimapNmax:
+ type: int?
+ inputBinding:
+ prefix: "--outFilterMultimapNmax"
+
+ OutFilterMismatchNmax:
+ type: int?
+ inputBinding:
+ prefix: "--outFilterMismatchNmax"
+
+ OutFilterMismatchNoverLmax:
+ type: double?
+ inputBinding:
+ prefix: "--outFilterMismatchNoverLmax"
+
+ OutReadsUnmapped:
+ type:
+ - "null"
+ - type: enum
+ symbols:
+ - None
+ - Fastx
+ inputBinding:
+ prefix: "--outReadsUnmapped"
+
+ OutSAMstrandField:
+ type:
+ - "null"
+ - type: enum
+ symbols:
+ - None
+ - intronMotif
+ inputBinding:
+ prefix: "--outSAMstrandField"
+
+ OutSAMunmapped:
+ type:
+ - "null"
+ - type: enum
+ symbols:
+ - None
+ - Within
+ - "Within KeepPairs"
+ inputBinding:
+ prefix: "--outSAMunmapped"
+
+ OutSAMmapqUnique:
+ type: int?
+ inputBinding:
+ prefix: "--outSAMmapqUnique"
+
+ OutSamMode:
+ type:
+ - "null"
+ - type: enum
+ symbols:
+ - None
+ - Full
+ - NoQS
+ inputBinding:
+ prefix: "--outSAMmode"
+
+ LimitOutSAMoneReadBytes:
+ type: int?
+ inputBinding:
+ prefix: "--limitOutSAMoneReadBytes"
+
+ OutFileNamePrefix:
+ type: string?
+ inputBinding:
+ prefix: "--outFileNamePrefix"
+
+ GenomeLoad:
+ type:
+ - "null"
+ - type: enum
+ symbols:
+ - LoadAndKeep
+ - LoadAndRemove
+ - LoadAndExit
+ - Remove
+ - NoSharedMemory
+ inputBinding:
+ prefix: "--genomeLoad"
+
+baseCommand: [STAR, --runMode, alignReads]
+
+outputs:
+ alignment:
+ type:
+ - File
+ outputBinding:
+ glob: "*.bam"
+ unmapped_reads:
+ type: ["null", File]
+ outputBinding:
+ glob: "Unmapped.out*"
+
+$namespaces:
+ edam: https://edamontology.org/
+$schemas:
+ - https://edamontology.org/EDAM_1.18.owl