class: Workflow
cwlVersion: v1.0
doc: Split reads in a BAM file by strands and index forward and reverse output BAM files
requirements:
 - class: ScatterFeatureRequirement
 - class: StepInputExpressionRequirement
 - class: InlineJavascriptRequirement
inputs:
   bamtools_reverse_filter_file:
     doc: JSON filter file for reverse strand used in bamtools (see bamtools-filter command)
     type: File
   bamtools_forward_filter_file:
     doc: JSON filter file for forward strand used in bamtools (see bamtools-filter command)
     type: File
   input_bam_files:
     type: File[]
   input_basenames:
     type: string[]
steps:
   split-bam-minus:
     run: ../quant/bamtools-filter.cwl
     scatterMethod: dotproduct
     scatter:
     - in
     - out
     in:
       script: bamtools_reverse_filter_file
       out:
         source: input_basenames
         valueFrom: $(self + ".Aligned.minus.bam")
       in:
         source: input_bam_files
         valueFrom: ${return [self]}
     out:
     - output_file
   index_minus_bam:
     run: ../map/samtools-index.cwl
     in:
       input_file: split-bam-minus/output_file
     scatter: input_file
     out:
     - indexed_file
   split-bam-plus:
     run: ../quant/bamtools-filter.cwl
     scatterMethod: dotproduct
     scatter:
     - in
     - out
     in:
       in:
         source: input_bam_files
         valueFrom: ${return [self]}
       out:
         source: input_basenames
         valueFrom: $(self + ".Aligned.plus.bam")
       script: bamtools_forward_filter_file
     out:
     - output_file
   index_plus_bam:
     run: ../map/samtools-index.cwl
     scatter: input_file
     in:
       input_file: split-bam-plus/output_file
     out:
     - indexed_file
outputs:
   bam_minus_files:
     doc: BAM files containing only reads in the reverse (minus) strand.
     type: File[]
     outputSource: index_minus_bam/indexed_file
   bam_plus_files:
     doc: BAM files containing only reads in the forward (plus) strand.
     type: File[]
     outputSource: index_plus_bam/indexed_file