class: Workflow
cwlVersion: v1.0
id: rd_connect
label: RD_Connect

inputs:
  - id: curl_reference_genome_url
    type: File
  - id: curl_fastq_urls
    type: File
  - id: curl_known_indels_url
    type: File
  - id: curl_known_sites_url
    type: File
  - id: readgroup_str
    type: string
  - id: chromosome
    type: string?
  - id: sample_name
    type: string
  - id: lftp_out_conf
    type: File

outputs:
  metrics:
    outputSource: picard_markduplicates/output_metrics
    type: File
  index:
    outputSource: samtools_index/index_fai
    type: File
  bam:
    outputSource: gatk-base_recalibration_print_reads/bqsr_bam
    type: File
  gvcf:
    outputSource: gatk_haplotype_caller/gvcf
    type: File
    
steps:
  - id: fastqs_in
    in:
      - id: curl_config_file
        source: curl_fastq_urls
    out: 
      - id: in_files
    run: curl.cwl

  - id: reference_in
    in:
      - id: curl_config_file
        source: curl_reference_genome_url
    out: 
      - id: in_files
    run: curl.cwl

  - id: known_indels_in
    in:
      - id: curl_config_file
        source: curl_known_indels_url
    out:
      - id: known_indels_file
    run: curl_indels.cwl

  - id: known_sites_in
    in:
      - id: curl_config_file
        source: curl_known_sites_url
    out:
      - id: known_sites_file
    run: curl_known_sites.cwl

  - id: unzipped_known_sites
    in:
      - id: known_sites_file
        source:
          - known_sites_in/known_sites_file
    out:
      - id: unzipped_known_sites_file
    run: gunzip_known_sites.cwl

  - id: gunzip
    in:
      - id: reference_file
        source:
          - reference_in/in_files
    out:
      - id: unzipped_fasta
    run: gunzip.cwl

  - id: picard_dictionary
    in:
      - id: reference_genome
        source:
          - gunzip/unzipped_fasta
    out:
      - id: dict
    run: picard_dictionary.cwl

  - id: cutadapt2
    in:
      - id: raw_sequences
        source:
          - fastqs_in/in_files
    out: 
      - id: trimmed_fastq
    run: cutadapt-v.1.18.cwl

  - id: bwa_index
    in:
      - id: reference_genome
        source:
          - gunzip/unzipped_fasta
    out:
      - id: output
    run: bwa-index.cwl

  - id: samtools_index
    in:
      - id: input
        source:
          - gunzip/unzipped_fasta
    out:
      - id: index_fai
    run: samtools_index.cwl


  - id: bwa_mem
    in:
      - id: trimmed_fastq
        source:
         - cutadapt2/trimmed_fastq
      - id: read_group
        source:
          - readgroup_str
      - id: sample_name
        source:
          - sample_name
      - id: reference_genome
        source:
          - bwa_index/output
    out:
      - id: aligned_sam
    run: bwa-mem.cwl

  - id: samtools_sort
    in:
      - id: input
        source:
          - bwa_mem/aligned_sam
    out:
      - id: sorted_bam
    run: samtools_sort_bam.cwl
   
  - id: picard_markduplicates
    in:
      - id: input
        source: 
          - samtools_sort/sorted_bam
    out:
      - id: md_bam
      - id: output_metrics
    run: picard_markduplicates.cwl
    label: picard-MD

  - id: gatk3-rtc
    in:
      - id: input
        source: 
          - picard_markduplicates/md_bam
      - id: reference_genome
        source: 
          - samtools_index/index_fai
      - id: dict
        source:
          - picard_dictionary/dict
      - id: known_indels
        source:
          - known_indels_in/known_indels_file
    out:
      - id: rtc_intervals_file
    run: gatk3-rtc.cwl
    label: gatk3-rtc

  - id: gatk-ir
    in:
      - id: input
        source: 
          - picard_markduplicates/md_bam
      - id: rtc_intervals
        source: 
          - gatk3-rtc/rtc_intervals_file
      - id: reference_genome
        source: 
           - samtools_index/index_fai
      - id: dict
        source:
          - picard_dictionary/dict
    out:
      - id: realigned_bam
    run: gatk-ir.cwl
    label: gatk-ir

  - id: gatk-base_recalibration
    in:
      - id: reference_genome
        source: 
          - samtools_index/index_fai
      - id: dict
        source:
          - picard_dictionary/dict
      - id: input
        source:
          - gatk-ir/realigned_bam
      - id: unzipped_known_sites_file
        source:
          - unzipped_known_sites/unzipped_known_sites_file
      - id: known_indels_file
        source:
          - known_indels_in/known_indels_file
    out:
      - id: br_model
    run: gatk-base_recalibration.cwl
    label: gatk-base_recalibration

  - id: gatk-base_recalibration_print_reads
    in:
      - id: reference_genome
        source: 
          - samtools_index/index_fai
      - id: dict
        source:
          - picard_dictionary/dict
      - id: input
        source:
          - gatk-ir/realigned_bam
      - id: br_model
        source:
          - gatk-base_recalibration/br_model
    out:
      - id: bqsr_bam
    run: gatk-base_recalibration_print_reads.cwl
    label: gatk-base_recalibration_print_reads


  - id: gatk_haplotype_caller
    in:
      - id: reference_genome
        source: 
          - samtools_index/index_fai
      - id: dict
        source:
          - picard_dictionary/dict
      - id: input
        source:
          - gatk-base_recalibration_print_reads/bqsr_bam
      - id: chromosome
        source: 
          - chromosome
    out:
      - id: gvcf
    run: gatk-haplotype_caller.cwl
    label: gatk-haplotype_caller

#  - id: lftp_out
#    in: 
#      - id: lftp_out_conf
#        source: lftp_out_conf
#      - id: files_to_send
#        source:
#          - picard_markduplicates/output_metrics
#          - samtools_index/index_fai
#      - id: bam
#        source:
#          - gatk-base_recalibration_print_reads/bqsr_bam
#      - id: gvcf
#        source:      
#          - gatk_haplotype_caller/gvcf
#    out: []
#    run: lftp.cwl

requirements:
  - class: MultipleInputFeatureRequirement