;;
;; fastq2fasta.cwl workflow
;;

(add-to-load-path "./scripts")

(use-modules (srfi srfi-26)
             (generate-cwl)
             (yaml))

(define threads
  (input "threads"
         #:type 'int
         #:label "number of threads"
         #:default 4))

(define ref-fasta
  (input "ref_fasta" #:type 'File))

(define sample-id
  (input "sample_id" #:type 'string))

(call-with-output-file "workflows/fastq2fasta/bwa-mem.cwl"
  (cut scm->yaml
    (clitool
     (list "bwa" "mem"
           "-t" threads
           "-o" (input "output_sam"
                       #:type 'string
                       #:label "sam file to output results to"
                       #:default "out.sam")
           "-R" (input "group_header_line"
                       #:type 'string?
                       #:label "read group header line such as '@RG\tID:foo\tSM:bar'")
           (input "index_base"
                  #:type 'File
                  #:label "fasta file for index basename"
                  #:other '((secondary-files . #(".amb" ".ann" ".bwt" ".pac" ".sa"))))
           (input "fastq_forward"
                  #:type 'File
                  #:label "input fastq file to map (single-end or forward for pair-end)")
           (input "fastq_reverse"
                  #:type 'File?
                  #:label "input fastq file to map (reverse for pair-end)"))
     #:outputs (list (output "output"
                             #:type 'File
                             #:binding '((glob . "$(inputs.output_sam)")))
                     (output "stdout" #:type 'stdout)
                     (output "stderr" #:type 'stderr))
     #:stdout "bwa-mem-stdout.log"
     #:stderr "bwa-mem-stderr.log"
     #:other '((requirements
                (Docker-requirement
                 (docker-pull . "quay.io/biocontainers/bwa:0.7.17--h84994c4_5")))))
    <>))

(call-with-output-file "workflows/fastq2fasta/samtools-view.cwl"
  (cut scm->yaml
    (clitool
     (list "samtools" "view"
           "-@" threads
           "-b" (input "output_bam"
                       #:type 'boolean
                       #:label "output BAM"
                       #:default #t)
           "-o" (input "output_filename"
                       #:type 'string
                       #:label "output file name"
                       #:default "aln.bam")
           (input "input_file"
                  #:type 'File
                  #:label "input file")
           "-h" (input "include_header"
                       #:type 'boolean
                       #:label "include the header in the output"
                       #:default #f)
           "-S" (input "ignore_previous_version"
                       #:type 'boolean
                       #:label "ignored for compatibility with previous samtools versions"
                       #:default #f)
           "-F" (input "filter_alignments"
                       #:type 'string?
                       #:label "Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' (i.e. /^0[0-7]+/) [0].")
           "-q" (input "skip_alignments"
                       #:type 'int?
                       #:label "Skip alignments with MAPQ smaller than INT [0]."))
     #:outputs (list (output "bam"
                             #:type 'File
                             #:binding '((glob . "$(inputs.output_filename)")))
                     (output "stdout" #:type 'stdout)
                     (output "stderr" #:type 'stderr))
     #:stdout "samtools-view-stdout.log"
     #:stderr "samtools-view-stderr.log"
     #:other '((doc . "samtools view to convert sam format to bam format")
               (requirements
                (Docker-requirement
                 (docker-pull . "quay.io/biocontainers/samtools:1.9--h8571acd_11")))))
    <>))

(call-with-output-file "workflows/fastq2fasta/samtools-sort.cwl"
  (cut scm->yaml
    (clitool
     (list "samtools" "sort"
           "-@" threads
           "-T" (input "tmpfile"
                       #:type 'string
                       #:label "Write temporary files to PREFIX.nnnn.bam"
                       #:default "sort.tmp")
           "-o" (input "output_bam"
                       #:type 'string
                       #:label "Write final output to FILENAME"
                       #:default "aln.sorted.bam")
           (input "input_bamfile"
                  #:type 'File
                  #:label "Input bamfile"))
     #:outputs (list (output "sorted_bam"
                             #:type 'File
                             #:binding '((glob . "$(inputs.output_bam)")))
                     (output "stdout" #:type 'stdout)
                     (output "stderr" #:type 'stderr))
     #:stdout "samtools-sort-stdout.log"
     #:stderr "samtools-sort-stderr.log"
     #:other '((doc . "samtools sort, sort given bam file")
               (requirements
                (Docker-requirement
                 (docker-pull . "quay.io/biocontainers/samtools:1.9--h8571acd_11")))))
    <>))

(call-with-output-file "workflows/fastq2fasta/freebayes.cwl"
  (cut scm->yaml
    (clitool
     (list "freebayes" "--ploidy" "1"
           "--bam" (input "bam" #:type 'File)
           "-f" ref-fasta)
     #:outputs (list (output "vcf" #:type 'stdout))
     #:stdout "var.vcf")
   <>))

(call-with-output-file "workflows/fastq2fasta/bcftools-view-exclude-ref.cwl"
  (cut scm->yaml
    (clitool
     (list "bcftools" "view" "--no-version" "-Ou"
           "-e'type=ref'" "--threads" threads
           (input "vcf" #:type 'File))
     #:outputs (list (output "bcf" #:type 'stdout))
     #:stdout "$(inputs.vcf.nameroot).without-ref.bcf")
    <>))

(call-with-output-file "workflows/fastq2fasta/bcftools-norm.cwl"
  (cut scm->yaml
    (clitool
     (list "bcftools" "norm" "-Ob"
           "-f" ref-fasta
           "-o" (input "output_name" #:type 'string #:default "normalized.bcf")
           "--threads" threads
           (input "bcf" #:type 'File))
     #:outputs (list (output "normalized_bcf"
                             #:type 'File
                             #:binding '((glob . "$(inputs.output_name)"))))
     #:other '((hints
                (Docker-requirement
                 (docker-pull . "quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0")))))
    <>))

(call-with-output-file "workflows/fastq2fasta/bcftools-index.cwl"
  (cut scm->yaml
    (clitool
     (list "bcftools" "index" (input "bcf" #:type 'File))
     #:outputs (list (output "indexed"
                             #:type 'File
                             #:binding '((glob . "$(inputs.bcf.basename)"))
                             #:other '((secondary-files . #(".csi")))))
     #:other '((hints
                (Docker-requirement
                 (docker-pull . "quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0"))
                (Initial-work-dir-requirement
                 (listing . #("$(inputs.bcf)"))))))
    <>))

(call-with-output-file "workflows/fastq2fasta/bcftools-view-qc.cwl"
  (cut scm->yaml
    (clitool
     (list "bcftools" "view" "-i" "'QUAL > 10 && GT=\"a\"'" "-Oz"
           "--threads" threads
           (input "bcf"
                  #:type 'File
                  #:other '((secondary-files . #(".csi")))))
     #:outputs (list (output "vcf" #:type 'stdout))
     #:other '((hints
                (Docker-requirement
                 (docker-pull . "quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0")))))
    <>))

(call-with-output-file "workflows/fastq2fasta/bcftools-consensus.cwl"
  (cut scm->yaml
    (clitool
     (list "bcftools" "consensus"
           "-i" "'QUAL > 10 && GT=\"a\"'" "-Hla"
           "-f" ref-fasta
           (input "vcf"
                  #:type 'File
                  #:other '((secondary-files . #(".csi")))))
     #:outputs (list (output "out_fasta" #:type 'stdout))
     #:stdout "sequence.fasta"
     #:other '((hints
                (Docker-requirement
                 (docker-pull . "quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0")))))
    <>))

(call-with-output-file "workflows/fastq2fasta/set-sample-id.cwl"
  (cut scm->yaml
    (clitool
     (list "sed" (input "fasta" #:type 'File))
     #:additional-inputs (list (input "sample_id" #:type 'string))
     #:outputs (list (output "out_fasta" #:type 'stdout))
     #:stdout "sequence.fasta"
     #:other '((arguments . #("s/^>.*/>$(inputs.sample_id)/g"))))
    <>))

(let ((fasta (input "fasta" #:type 'File)))
  (call-with-output-file "workflows/fastq2fasta/bam2fasta.cwl"
    (cut scm->yaml
      (workflow
       (list (step "freebayes" "freebayes.cwl"
                   `((bam . ,(input "bam" #:type 'File))
                     (ref_fasta . ,fasta))
                   (list "vcf"))
             (step "bcftools_view_exclude_ref" "bcftools-view-exclude-ref.cwl"
                   `((vcf . "freebayes/vcf")
                     (threads . ,threads))
                   (list "bcf"))
             (step "bcftools_norm" "bcftools-norm.cwl"
                   `((ref_fasta . ,fasta)
                     (bcf . "bcftools_view_exclude_ref/bcf")
                     (threads . ,threads))
                   (list "normalized_bcf"))
             (step "bcftools_index_after_normalization" "bcftools-index.cwl"
                   '((bcf . "bcftools_norm/normalized_bcf"))
                   (list "indexed"))
             (step "bcftools_view_qc" "bcftools-view-qc.cwl"
                   `((bcf . "bcftools_index_after_normalization/indexed")
                     (threads . ,threads))
                   (list "vcf"))
             (step "bcftools_index_after_qc" "bcftools-index.cwl"
                   '((bcf . "bcftools_view_qc/vcf"))
                   (list "indexed"))
             (step "bcftools_consensus" "bcftools-consensus.cwl"
                   `((ref_fasta . ,fasta)
                     (vcf . "bcftools_index_after_qc/indexed"))
                   (list "out_fasta"))
             (step "set_sample_id" "set-sample-id.cwl"
                   `((fasta . "bcftools_consensus/out_fasta")
                     (sample_id . ,sample-id))
                   (list "out_fasta")))
       (list (workflow-output "out_fasta"
                              #:type 'File
                              #:source "set_sample_id/out_fasta")))
      <>)))

(let ((ref-fasta (input "ref_fasta"
                        #:type 'File
                        #:other '((secondary-files . #(".amb" ".ann" ".bwt" ".pac" ".sa" ".fai"))))))
  (call-with-output-file "workflows/fastq2fasta/fastq2fasta.cwl"
    (cut scm->yaml
      (workflow
       (list (step "bwa-mem" "bwa-mem.cwl"
                   `((threads . ,threads)
                     (fastq_forward . ,(input "fastq_forward" #:type 'File))
                     (fastq_reverse . ,(input "fastq_reverse" #:type 'File?))
                     (index_base . ,ref-fasta))
                   (list "output"))
             (step "samtools-view" "samtools-view.cwl"
                   `((threads . ,threads)
                     (input_file . "bwa-mem/output"))
                   (list "bam"))
             (step "samtools-sort" "samtools-sort.cwl"
                   `((input_bamfile . "samtools-view/bam")
                     (threads . ,threads))
                   (list "sorted_bam"))
             (step "bam2fasta" "bam2fasta.cwl"
                   `((bam . "samtools-sort/sorted_bam")
                     (fasta . ,ref-fasta)
                     (threads . ,threads)
                     (sample_id . ,sample-id))
                   (list "out_fasta")))
       (list (workflow-output "out_fasta"
                              #:type 'File
                              #:source "bam2fasta/out_fasta")
             (workflow-output "out_metadata"
                              #:type 'File?
                              #:source (input "metadata" #:type 'File?)))
       #:other '((requirements (Subworkflow-feature-requirement))
                 (hints (Resource-requirement (ram-min . 3000)))))
      <>)))