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|
;;
;; 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)))))
<>)))
|
