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input {
String? preCommand
File? short1
File? short2
File? unpaired
File? long
String out
Int? verbosity
Int? minFastaLength
Int? keep
Boolean? vcf
Int? threads = 1
Int? memory = 4
String? mode
Float? minBridgeQual
Int? linearSeqs
File? spadesPath
Boolean? noCorrect
Float? minKmerFrac
Float? maxKmerFrac
Int? kmerCount
Float? depthFilter
Boolean? noMiniasm
File? raconPath
File? existingLongReadAssembly
Boolean? noRotate
File? startGenes
Float? startGeneId
Float? startGeneCov
String? makeblastdbPath
File? tblastnPath
Boolean? noPilon
File? bowtie2Path
File? bowtie2buildPath
File? samtoolsPath
File? pilonPath
File? javaPath
Int? minPolishSize
File? bcftoolsPath
Int? minComponentSize
Int? minDeadEndSize
File? contamination
String? scores
String? lowScore
}
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~{"--short1 " + short1} \
~{"--short2 " + short2} \
~{"--unpaired " + unpaired} \
~{"--long " + long} \
--out ~{out} \
~{"--min_fasta_length " + minFastaLength} \
~{"--keep " + keep } \
~{true="--vcf" false="" vcf } \
~{"--threads " + threads } \
~{"--mode " + mode } \
~{"--min_bridge_qual " + minBridgeQual } \
~{"--linear_seqs " + linearSeqs } \
~{"--spades_path " + spadesPath } \
~{true="--no_correct" false="" noCorrect } \
~{"--min_kmer_frac " + minKmerFrac } \
~{"--max_kmer_frac " + maxKmerFrac } \
~{"--kmer_count " + kmerCount } \
~{"--depth_filter " + depthFilter } \
~{true="--no_miniasm" false="" noMiniasm } \
~{"--racon_path " + raconPath } \
~{"--existing_long_read_assembly " + existingLongReadAssembly } \
~{true="--no_rotate" false="" noRotate } \
~{"--start_genes " + startGenes } \
~{"--start_gene_id " + startGeneId } \
~{"--start_gene_cov " + startGeneCov } \
~{"--makeblastdb_path " + makeblastdbPath } \
~{"--tblastn_path " + tblastnPath } \
~{true="--no_pilon" false="" noPilon } \
~{"--bowtie2_path " + bowtie2Path } \
~{"--bowtie2_build_path " + bowtie2buildPath } \
~{"--samtools_path " + samtoolsPath } \
~{"--pilon_path " + pilonPath } \
~{"--java_path " + javaPath } \
~{"--min_polish_size " + minPolishSize } \
~{"--bcftools_path " + bcftoolsPath } \
~{"--min_component_size " + minComponentSize } \
~{"--min_dead_end_size " + minDeadEndSize } \
~{"--contamination " + contamination } \
~{"--scores " + scores } \
~{"--low_score " + lowScore }
output {
File assemblyFasta = out + "/assembly.fasta"
File assemblyGfa = out + "/assembly.gfa"
File log = out + "/unicycler.log"
}
cpu: select_first([threads])
memory: select_first([memory])