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;; An implementation of the pangenome graph builder shell script at
;; https://github.com/pangenome/pggb in ccwl
(define wfmash
(command #:inputs
(input-fasta #:label "input FASTA/FASTQ file")
(segment-length #:type int)
(block-length #:type int)
(no-merge-segments #:type boolean?)
(no-split #:type boolean?)
(map-pct-id #:type float)
(n-secondary #:type int)
(mash-kmer #:type int #:default 16)
(threads #:type int #:default 1)
#:run "wfmash" ("-s" segment-length) ("-l" block-length) ("-M" no-merge-segments)
("-N" no-split) ("-p" map-pct-id) ("-n" n-secondary) ("-k" mash-kmer) ("-t" threads)
input-fasta input-fasta
#:outputs (mapper-out #:type stdout)))
(define seqwish
(command #:inputs
(input-fasta #:label "input FASTA/FASTQ file")
mapper-out
(min-match-len #:type int #:default 19)
(transclose-batch #:type int #:default 1000000)
(threads #:type int #:default 1)
#:run "seqwish" "-t" threads "-s" input-fasta "-p" mapper-out "-k" min-match-len
"-g" "seqwish.gfa" "-B" transclose-batch "-P"
#:outputs (seqwish-out #:binding '((glob . "seqwish.gfa")))))
(define smoothxg
(command #:inputs
seqwish-out
(block-weight-max #:type int #:default 10000)
(block-id-min #:type int #:default 0)
(ratio-contain #:type int #:default 0)
(path-jump-max #:type int #:default 5000)
(edge-jump-max #:type int #:default 5000)
(poa-length-max #:type int #:default 10000)
(poa-params #:type string #:default "1,4,6,2,26,1")
(consensus-spec #:type string #:default "10,100,1000,10000")
(threads #:type int #:default 1)
#:run "smoothxg" ("-t" threads) ("-g" seqwish-out) ("-w" block-weight-max) "-M"
"-J" "0.7" "-K" "-G" "150" ("-I" block-id-min) ("-j" path-jump-max)
("-e" edge-jump-max) ("-l" poa-length-max) ("-p" poa-params)
#:outputs
(smoothxg-graph #:binding '((glob . "smoothxg_out.gfa")))
(smoothxg-consensus #:binding '((glob . "smoothxg_out.consensus@10__y_0_1000000.gfa")))
(smoothxg-alignment #:binding '((glob . "smoothxg_out.maf")))))
(define odgi-build
(command #:inputs
(threads #:type int #:default 1)
smoothxg-graph
#:run "odgi" "build" ("-t" threads) "-P" ("-g" smoothxg-graph) "-o" "odgi_out.og"
#:outputs (odgi-out #:binding '((glob . "odgi_out.og")))))
(workflow ((segment-length #:type int
#:label "segment length for mapping")
(block-length #:type int
#:label "minimum block length filter for mapping")
(no-merge-segments #:type boolean?
#:label "do not merge successive mappings")
(no-split #:type boolean?
#:label "disable splitting of input sequences during mapping")
(map-pct-id #:type float
#:label "percent identity in the wfmash or edyeet mashmap step")
(n-secondary #:type int
#:label "number of secondary mappings to retain in 'map' filter mode")
(mash-kmer #:type int
#:label "kmer size for mashmap"
#:default 16)
(input-fasta #:label "input FASTA/FASTQ file")
(min-match-len #:type int
#:label "ignore exact matches below this length"
#:default 19)
(transclose-batch #:type int
#:label "number of bp to use for transitive closure batch"
#:default 1000000)
(block-weight-max #:type int
#:label "maximum seed sequence in block"
#:default 10000)
(block-id-min #:type int
#:label "split blocks into groups connected by this identity threshold"
#:default 0)
(ratio-contain #:type int
#:label "minimum short length / long length ratio to compare sequences for the containment metric in the clustering"
#:default 0)
(path-jump-max #:type int
#:label "maximum path jump to include in block"
#:default 5000)
(edge-jump-max #:type int
#:label "maximum edge jump before breaking"
#:default 5000)
(poa-length-max #:type int
#:label "maximum sequence length to put into POA"
#:default 10000)
(poa-params #:type string
#:label "score parameters for POA in the form of match,mismatch,gap1,ext1,gap2,ext2"
#:default "1,4,6,2,26,1")
(consensus-spec #:type string
#:label "consensus graph specification: write the consensus graph to BASENAME.cons_[spec].gfa; where each spec contains at least a min_len parameter (which defines the length of divergences from consensus paths to preserve in the output), optionally a file containing reference paths to preserve in the output, a flag (y/n) indicating whether we should also use the POA consensus paths, a minimum coverage of consensus paths to retain (min_cov), and a maximum allele length (max_len, defaults to 1e6); implies -a; example: cons,100,1000:refs1.txt:n,1000:refs2.txt:y:2.3:1000000,10000"
#:default "10,100,1000,10000")
(threads #:type int
#:label "number of compute threads to use in parallel steps"
#:default 1))
(pipe (wfmash #:input-fasta input-fasta
#:segment-length segment-length
#:block-length block-length
#:no-merge-segments no-merge-segments
#:no-split no-split
#:map-pct-id map-pct-id
#:n-secondary n-secondary
#:mash-kmer mash-kmer
#:threads threads)
(seqwish #:input-fasta input-fasta
#:mapper-out mapper-out
#:min-match-len min-match-len
#:transclose-batch transclose-batch
#:threads threads)
(smoothxg #:seqwish-out seqwish-out
#:block-weight-max block-weight-max
#:block-id-min block-id-min
#:ratio-contain ratio-contain
#:path-jump-max path-jump-max
#:edge-jump-max edge-jump-max
#:poa-length-max poa-length-max
#:poa-params poa-params
#:consensus-spec consensus-spec
#:threads threads)
(odgi-build #:smoothxg-graph smoothxg-graph
#:threads threads)))
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