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;;
;; fastq2fasta.cwl workflow
;;
(use-modules (ccwl ccwl))
(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 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 fastq2fasta
(workflow "fastq2fasta"
(list (pipeline "bwa_mem_to_normalized"
(list (command "bwa_mem"
(list "bwa" "mem" "-t" threads
ref-fasta fastq-forward fastq-reverse))
(command "samtools_view"
(list "samtools" "view" "-b" "-@" threads "-"))
(command "samtools_sort"
(list "samtools" "sort" "-T" "sort.tmp" "-@" threads "-"))
(command "freebayes"
(list "freebayes" "--ploidy" "1" "--stdin" "-f" ref-fasta))
(command "bcftools_view_exclude_ref"
(list "bcftools" "view"
"--no-version" "-Ou" "-e'type=ref'"
"--threads" threads "-"))
(command "bcftools_norm"
(list "bcftools" "norm" "-Ob"
"-f" ref-fasta "--threads" threads "-")
#:other '((stdout . "normalized.bcf"))))
(list (output "normalized"
#:type 'File
#:source "bcftools_norm/stdout")))
(command "bcftools_index_after_normalization"
(list "bcftools" "index" (input "normalized" #:type 'File))
#:outputs (list (output "index_after_normalization"
#:type 'File
#:binding '((glob . "$(inputs.normalized.basename)"))
#:other '((secondary-files . #(".csi")))))
#:other `((hints (Initial-work-dir-requirement
(listing . #("$(inputs.normalized)"))))))
(command "bcftools_view_qc"
(list "bcftools" "view"
"-i" "'QUAL > 10 && GT=\"a\"'"
"-Oz" "--threads" threads
(input "index_after_normalization"
#:type 'File
#:other '((secondary-files . #(".csi")))))
#:outputs (list (output "bcftools_view_qc_output_vcf" #:type 'stdout))
#:other '((stdout . "bcftools_view_output.vcf.gz")))
(command "bcftools_index_after_qc"
(list "bcftools" "index" (input "bcftools_view_qc_output_vcf" #:type 'File))
#:outputs (list (output "index_after_qc"
#:type 'File
#:binding '((glob . "$(inputs.bcftools_view_qc_output_vcf.basename)"))
#:other '((secondary-files . #(".csi")))))
#:other `((hints (Initial-work-dir-requirement
(listing . #("$(inputs.bcftools_view_qc_output_vcf)"))))))
(pipeline "consensus"
(list (command "bcftools_consensus"
(list "bcftools" "consensus"
"-i" "'QUAL > 10 && GT=\"a\"'"
"-Hla" "-f" ref-fasta
(input "index_after_qc"
#:type 'File
#:other '((secondary-files . #(".csi"))))))
(command "set_sample_id"
(list "sed" "s/^>.*/>$(inputs.sample_id)/g")
#:additional-inputs (list sample-id)))
(list (output "out_fasta"
#:type 'File
#:source "set_sample_id/stdout"))))
(list (output "out_fasta"
#:type 'File
#:source "consensus/out_fasta"))))
(write-cwl fastq2fasta "workflows/fastq2fasta/fastq2fasta.cwl")
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