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;;
;; fastq2fasta.cwl workflow
;;
(use-modules (srfi srfi-26)
(generate-cwl generate-cwl)
(generate-cwl yaml))
(define threads
(input "threads"
#:type 'int
#:label "number of threads"
#:default 4))
(define ref-fasta
(input "ref_fasta"
#:type 'File
#:other '((secondary-files . #(".amb" ".ann" ".bwt" ".pac" ".sa")))))
(define output-sam
(input "output_sam"
#:type 'string
#:label "sam file to output results to"
#:default "out.sam"))
(define group-header-line
(input "group_header_line"
#:type 'string?
#:label "read group header line such as '@RG\tID:foo\tSM:bar'"))
(define fastq-forward
(input "fastq_forward"
#:type 'File
#:label "input fastq file to map (single-end or forward for pair-end)"))
(define fastq-reverse
(input "fastq_reverse"
#:type 'File?
#:label "input fastq file to map (reverse for pair-end)"))
(define sample-id
(input "sample_id" #:type 'string))
(define bwa-docker
'(Docker-requirement
(docker-pull . "quay.io/biocontainers/bwa:0.7.17--h84994c4_5")))
(define samtools-docker
'(Docker-requirement
(docker-pull . "quay.io/biocontainers/samtools:1.9--h8571acd_11")))
(define bcftools-docker
'(Docker-requirement
(docker-pull . "quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0")))
(define fastq2fasta
(workflow
(list (clitool-step "bwa_mem"
(list "bwa" "mem"
"-t" threads
"-o" output-sam
"-R" group-header-line
ref-fasta
fastq-forward
fastq-reverse)
#:outputs (list (output "output"
#:type 'File
#:binding '((glob . "$(inputs.output_sam)"))))
#:other `((requirements ,bwa-docker)))
(clitool-step "samtools_view"
(list "samtools" "view"
"-b"
"-o" "aln.bam"
"-@" threads
(intermediate (input "input_file"
#:type 'File
#:label "input file")
"bwa_mem/output"))
#:outputs (list (output "bam"
#:type 'File
#:binding '((glob . "aln.bam"))))
#:other `((doc . "samtools view to convert sam format to bam format")
(requirements ,samtools-docker)))
(clitool-step "samtools_sort"
(list "samtools" "sort"
"-T" "sort.tmp"
"-o" "aln.sorted.bam"
"-@" threads
(intermediate (input "input_bamfile"
#:type 'File
#:label "Input bamfile")
"samtools_view/bam"))
#:outputs (list (output "sorted_bam"
#:type 'File
#:binding '((glob . "aln.sorted.bam"))))
#:other `((doc . "samtools sort, sort given bam file")
(requirements ,samtools-docker)))
(clitool-step "freebayes"
(list "freebayes"
"--ploidy" "1"
"--bam" (intermediate (input "bam" #:type 'File)
"samtools_sort/sorted_bam")
"-f" ref-fasta)
#:outputs (list (output "vcf" #:type 'stdout))
#:stdout "var.vcf")
(clitool-step "bcftools_view_exclude_ref"
(list "bcftools" "view"
"--no-version" "-Ou"
"-e'type=ref'"
"--threads" threads
(intermediate (input "vcf" #:type 'File)
"freebayes/vcf"))
#:outputs (list (output "bcf" #:type 'stdout))
#:other `((hints ,bcftools-docker)))
(clitool-step "bcftools_norm"
(list "bcftools" "norm"
"-Ob"
"-o" "normalized.bcf"
"-f" ref-fasta
"--threads" threads
(intermediate (input "bcf" #:type 'File)
"bcftools_view_exclude_ref/bcf"))
#:outputs (list (output "normalized_bcf"
#:type 'File
#:binding '((glob . "normalized.bcf"))))
#:other `((hints ,bcftools-docker)))
(clitool-step "bcftools_index_after_normalization"
(list "bcftools" "index"
(intermediate (input "bcf" #:type 'File)
"bcftools_norm/normalized_bcf"))
#:outputs (list (output "indexed"
#:type 'File
#:binding '((glob . "$(inputs.bcf.basename)"))
#:other '((secondary-files . #(".csi")))))
#:other `((hints ,bcftools-docker
(Initial-work-dir-requirement
(listing . #("$(inputs.bcf)"))))))
(clitool-step "bcftools_view_qc"
(list "bcftools" "view"
"-i" "'QUAL > 10 && GT=\"a\"'"
"-Oz"
"--threads" threads
(intermediate (input "bcf"
#:type 'File
#:other '((secondary-files . #(".csi"))))
"bcftools_index_after_normalization/indexed"))
#:outputs (list (output "vcf" #:type 'stdout))
#:other `((hints ,bcftools-docker)))
(clitool-step "bcftools_index_after_qc"
(list "bcftools" "index"
(intermediate (input "bcf" #:type 'File)
"bcftools_view_qc/vcf"))
#:outputs (list (output "indexed"
#:type 'File
#:binding '((glob . "$(inputs.bcf.basename)"))
#:other '((secondary-files . #(".csi")))))
#:other `((hints ,bcftools-docker
(Initial-work-dir-requirement
(listing . #("$(inputs.bcf)"))))))
(clitool-step "bcftools_consensus"
(list "bcftools" "consensus"
"-i" "'QUAL > 10 && GT=\"a\"'"
"-Hla"
"-f" ref-fasta
(intermediate (input "vcf"
#:type 'File
#:other '((secondary-files . #(".csi"))))
"bcftools_index_after_qc/indexed"))
#:outputs (list (output "out_fasta" #:type 'stdout))
#:stdout "sequence.fasta"
#:other `((hints ,bcftools-docker)))
(clitool-step "set_sample_id"
(list "sed" (intermediate (input "fasta" #:type 'File)
"bcftools_consensus/out_fasta"))
#:additional-inputs (list sample-id)
#:outputs (list (output "out_fasta" #:type 'stdout))
#:stdout "sequence.fasta"
#:other '((arguments . #("s/^>.*/>$(inputs.sample_id)/g")))))
(list (workflow-output "out_fasta"
#:type 'File
#:source "set_sample_id/out_fasta"))))
(call-with-output-file "workflows/fastq2fasta/fastq2fasta.cwl"
(cut scm->yaml fastq2fasta <>))
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