#!/usr/bin/env cwltool

doc: |
  The "main" workflow. Takes fastq files generated using the seCLIP protocol 
  (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991800/) and outputs 
  candidate RBP binding regions (peaks). 

  runs:
    wf_get_peaks_se.cwl through scatter across multiple samples.

cwlVersion: v1.0
class: Workflow

requirements:
  - class: StepInputExpressionRequirement
  - class: SubworkflowFeatureRequirement
  - class: ScatterFeatureRequirement
  - class: MultipleInputFeatureRequirement

inputs:
  dataset:
    type: string

  speciesGenomeDir:
    type: Directory

  repeatElementGenomeDir:
    type: Directory

  species:
    type: string

  chrom_sizes:
    type: File

  samples:
    type:
      type: array
      items:
        type: array
        items:
          type: record
          fields:
            read1:
              type: File
            name:
              type: string
            adapters:
              type: File

  blacklist_file: 
    type: File

outputs:


  ### DEMULTIPLEXED READ OUTPUTS ###


  output_ip_b1_demuxed_fastq_r1:
    type: File[]
    outputSource: step_get_peaks/output_ip_b1_demuxed_fastq_r1

  output_input_b1_demuxed_fastq_r1:
    type: File[]
    outputSource: step_get_peaks/output_input_b1_demuxed_fastq_r1


  ### TRIMMED ROUND1 OUTPUTS ###


  output_ip_b1_trimx1_fastq:
    type:
      type: array
      items:
        type: array
        items: File
    outputSource: step_get_peaks/output_ip_b1_trimx1_fastq
  output_ip_b1_trimx1_metrics:
    type: File[]
    outputSource: step_get_peaks/output_ip_b1_trimx1_metrics

  output_input_b1_trimx1_fastq:
    type:
      type: array
      items:
        type: array
        items: File
    outputSource: step_get_peaks/output_input_b1_trimx1_fastq
  output_input_b1_trimx1_metrics:
    type: File[]
    outputSource: step_get_peaks/output_input_b1_trimx1_metrics


  ### FASTQC ROUND1 OUTPUTS ###
  
  
  output_ip_b1_trimx1_fastqc_report:
    type: File[]
    outputSource: step_get_peaks/output_ip_b1_trimx1_fastqc_report
  output_ip_b1_trimx1_fastqc_stats:
    type: File[]
    outputSource: step_get_peaks/output_ip_b1_trimx1_fastqc_stats
  output_input_b1_trimx1_fastqc_report:
    type: File[]
    outputSource: step_get_peaks/output_input_b1_trimx1_fastqc_report
  output_input_b1_trimx1_fastqc_stats:
    type: File[]
    outputSource: step_get_peaks/output_input_b1_trimx1_fastqc_stats


  ### TRIMMED ROUND2 OUTPUTS ###


  output_ip_b1_trimx2_fastq:
    type:
      type: array
      items:
        type: array
        items: File
    outputSource: step_get_peaks/output_ip_b1_trimx2_fastq
  output_ip_b1_trimx2_metrics:
    type: File[]
    outputSource: step_get_peaks/output_ip_b1_trimx2_metrics
  
  output_input_b1_trimx2_fastq:
    type:
      type: array
      items:
        type: array
        items: File
    outputSource: step_get_peaks/output_input_b1_trimx2_fastq
  output_input_b1_trimx2_metrics:
    type: File[]
    outputSource: step_get_peaks/output_input_b1_trimx2_metrics


  ### FASTQC ROUND2 OUTPUTS ###
  
  
  output_ip_b1_trimx2_fastqc_report:
    type: File[]
    outputSource: step_get_peaks/output_ip_b1_trimx2_fastqc_report
  output_ip_b1_trimx2_fastqc_stats:
    type: File[]
    outputSource: step_get_peaks/output_ip_b1_trimx2_fastqc_stats

  output_input_b1_trimx2_fastqc_report:
    type: File[]
    outputSource: step_get_peaks/output_input_b1_trimx2_fastqc_report
  output_input_b1_trimx2_fastqc_stats:
    type: File[]
    outputSource: step_get_peaks/output_input_b1_trimx2_fastqc_stats
    
    
  ### REPEAT MAPPING OUTPUTS ###
  
  
  output_ip_b1_maprepeats_mapped_to_genome:
    type: File[]
    outputSource: step_get_peaks/output_ip_b1_maprepeats_mapped_to_genome
  output_ip_b1_maprepeats_stats:
    type: File[]
    outputSource: step_get_peaks/output_ip_b1_maprepeats_stats
  output_ip_b1_maprepeats_star_settings:
    type: File[]
    outputSource: step_get_peaks/output_ip_b1_maprepeats_star_settings
  output_ip_b1_sorted_unmapped_fastq:
    type: File[]
    outputSource: step_get_peaks/output_ip_b1_sorted_unmapped_fastq

  output_input_b1_maprepeats_mapped_to_genome:
    type: File[]
    outputSource: step_get_peaks/output_input_b1_maprepeats_mapped_to_genome
  output_input_b1_maprepeats_stats:
    type: File[]
    outputSource: step_get_peaks/output_input_b1_maprepeats_stats
  output_input_b1_maprepeats_star_settings:
    type: File[]
    outputSource: step_get_peaks/output_input_b1_maprepeats_star_settings
  output_input_b1_sorted_unmapped_fastq:
    type: File[]
    outputSource: step_get_peaks/output_input_b1_sorted_unmapped_fastq


  ### GENOME MAPPING OUTPUTS ###


  output_ip_b1_mapgenome_mapped_to_genome:
    type: File[]
    outputSource: step_get_peaks/output_ip_b1_mapgenome_mapped_to_genome
  output_ip_b1_mapgenome_stats:
    type: File[]
    outputSource: step_get_peaks/output_ip_b1_mapgenome_stats
  output_ip_b1_mapgenome_star_settings:
    type: File[]
    outputSource: step_get_peaks/output_ip_b1_mapgenome_star_settings

  output_input_b1_mapgenome_mapped_to_genome:
    type: File[]
    outputSource: step_get_peaks/output_input_b1_mapgenome_mapped_to_genome
  output_input_b1_mapgenome_stats:
    type: File[]
    outputSource: step_get_peaks/output_input_b1_mapgenome_stats
  output_input_b1_mapgenome_star_settings:
    type: File[]
    outputSource: step_get_peaks/output_input_b1_mapgenome_star_settings


  ### DUPLICATE REMOVAL OUTPUTS ###


  output_ip_b1_pre_rmdup_sorted_bam:
    type: File[]
    outputSource: step_get_peaks/output_ip_b1_pre_rmdup_sorted_bam
  # output_ip_b1_barcodecollapsese_metrics:
  #   type: File[]
  #   outputSource: step_get_peaks/output_ip_b1_barcodecollapsese_metrics
  output_ip_b1_rmdup_sorted_bam:
    type: File[]
    outputSource: step_get_peaks/output_ip_b1_rmdup_sorted_bam

  output_input_b1_pre_rmdup_sorted_bam:
    type: File[]
    outputSource: step_get_peaks/output_input_b1_pre_rmdup_sorted_bam
  # output_input_b1_barcodecollapsese_metrics:
  #   type: File[]
  #   outputSource: step_get_peaks/output_input_b1_barcodecollapsese_metrics
  output_input_b1_rmdup_sorted_bam:
    type: File[]
    outputSource: step_get_peaks/output_input_b1_rmdup_sorted_bam


  ### BIGWIG FILES ###


  output_ip_pos_bw:
    type: File[]
    outputSource: step_get_peaks/output_ip_pos_bw
  output_ip_neg_bw:
    type: File[]
    outputSource: step_get_peaks/output_ip_neg_bw
  output_input_pos_bw:
    type: File[]
    outputSource: step_get_peaks/output_input_pos_bw
  output_input_neg_bw:
    type: File[]
    outputSource: step_get_peaks/output_input_neg_bw


  ### PEAK OUTPUTS ###


  output_clipper_bed:
    type: File[]
    outputSource: step_get_peaks/output_clipper_bed
  output_inputnormed_peaks:
    type: File[]
    outputSource: step_get_peaks/output_inputnormed_peaks
  output_compressed_peaks:
    type: File[]
    outputSource: step_get_peaks/output_compressed_peaks


  ### DOWNSTREAM OUTPUTS ###


  output_blacklist_removed_bed:
    type: File[]
    outputSource: step_get_peaks/output_blacklist_removed_bed
  output_narrowpeak:
    type: File[]
    outputSource: step_get_peaks/output_narrowpeak
  output_fixed_bed:
    type: File[]
    outputSource: step_get_peaks/output_fixed_bed
  output_bigbed:
    type: File[]
    outputSource: step_get_peaks/output_bigbed
  output_entropynum:
    type: File[]
    outputSource: step_get_peaks/output_entropynum
    
steps:

  step_get_peaks:
    run: wf_get_peaks_nostats_se.cwl
    scatter: sample
    in:
      dataset: dataset
      speciesGenomeDir: speciesGenomeDir
      repeatElementGenomeDir: repeatElementGenomeDir
      species: species
      chrom_sizes: chrom_sizes
      sample: samples
      blacklist_file: blacklist_file
    out: [
      output_ip_b1_demuxed_fastq_r1,
      output_input_b1_demuxed_fastq_r1,
      output_ip_b1_trimx1_fastq,
      output_ip_b1_trimx1_metrics,
      output_ip_b1_trimx1_fastqc_report,
      output_ip_b1_trimx1_fastqc_stats,
      output_input_b1_trimx1_fastq,
      output_input_b1_trimx1_metrics,
      output_input_b1_trimx1_fastqc_report,
      output_input_b1_trimx1_fastqc_stats,
      output_ip_b1_trimx2_fastq,
      output_ip_b1_trimx2_metrics,
      output_ip_b1_trimx2_fastqc_report,
      output_ip_b1_trimx2_fastqc_stats,
      output_input_b1_trimx2_fastq,
      output_input_b1_trimx2_metrics,
      output_input_b1_trimx2_fastqc_report,
      output_input_b1_trimx2_fastqc_stats,
      output_ip_b1_maprepeats_mapped_to_genome,
      output_ip_b1_maprepeats_stats,
      output_ip_b1_maprepeats_star_settings,
      output_ip_b1_sorted_unmapped_fastq,
      output_input_b1_maprepeats_mapped_to_genome,
      output_input_b1_maprepeats_stats,
      output_input_b1_maprepeats_star_settings,
      output_input_b1_sorted_unmapped_fastq,
      output_ip_b1_mapgenome_mapped_to_genome,
      output_ip_b1_mapgenome_stats,
      output_ip_b1_mapgenome_star_settings,
      output_ip_b1_pre_rmdup_sorted_bam,
      # output_ip_b1_barcodecollapsese_metrics,
      output_ip_b1_rmdup_sorted_bam,
      output_input_b1_mapgenome_mapped_to_genome,
      output_input_b1_mapgenome_stats,
      output_input_b1_mapgenome_star_settings,
      output_input_b1_pre_rmdup_sorted_bam,
      # output_input_b1_barcodecollapsese_metrics,
      output_input_b1_rmdup_sorted_bam,
      output_ip_pos_bw,
      output_ip_neg_bw,
      output_input_pos_bw,
      output_input_neg_bw,
      output_clipper_bed,
      output_inputnormed_peaks,
      output_compressed_peaks,
      output_blacklist_removed_bed,
      output_narrowpeak,
      output_fixed_bed,
      output_bigbed,
      output_entropynum
    ]