Skip to content
Snippets Groups Projects
Commit 91da0d8f authored by Ruben Vorderman's avatar Ruben Vorderman
Browse files

unicycler to 1.0

parent ebc94bdb
No related branches found
No related tags found
1 merge request!34Move all files to version 1.0
Hide whitespace changes
Inline Side-by-side
spades.wdl
+ 2
− 2
View file @ 91da0d8f
......@@ -24,14 +24,14 @@ task spades {
Boolean? disableGzipOutput
Boolean? disableRepeatResolution
File? dataset
Int? threads
Int? threads = 1
Float? memoryGb
File? tmpDir
String? k
Float? covCutoff
Int? phredOffset
}
Int finalThreads = select_first([threads,1])
Int finalThreads = select_first([threads])
Float totalMemory = select_first([memoryGb, finalThreads * 16.0])
Int finalMemory = ceil(totalMemory)
Int clusterMemory = ceil(totalMemory / finalThreads)
......
unicycler.wdl
+ 91
− 89
View file @ 91da0d8f
version 1.0
task unicycler {
String? preCommand
File? short1
File? short2
File? unpaired
File? long
String out
Int? verbosity
Int? minFastaLength
Int? keep
Boolean? vcf
Int? threads
Int? memory
Int finalThreads = select_first(threads, 1)
Int finalMemory = select_first(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
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
}
command {
set -e -o pipefail
mkdir -p ${out}
${preCommand}
mkdir -p ~{out}
~{preCommand}
unicycler \
${"--short1 " + short1} \
${"--short2 " + short2} \
${"--unpaired " + unpaired} \
${"--long " + long} \
--out ${out} \
${"--min_fasta_length " + minFastaLength} \
${"--keep " + keep } \
${true="--vcf" false="" vcf } \
${"--threads " + finalThreads } \
${"--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 }
~{"--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"
......@@ -96,7 +98,7 @@ task unicycler {
File log = out + "/unicycler.log"
}
runtime {
cpu: finalThreads
memory: finalMemory
cpu: select_first([threads])
memory: select_first([memory])
}
}
\ No newline at end of file
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment