add spades task

spades.wdl

+task spades {
+    String outputDir
+    String? preCommand
+    File? read1
+    File? read2
+    File? singleRead
+    File? interlacedReads
+    File? sangerReads
+    File? pacbioReads
+    File? nanoporeReads
+    File? tslrContigs
+    File? trustedContigs
+    File? untrustedContigs
+    Boolean? singleCell
+    Boolean? metagenomic
+    Boolean? rna
+    Boolean? plasmid
+    Boolean? ionTorrent
+    Boolean? onlyErrorCorrection
+    Boolean? onlyAssembler
+    Boolean? careful
+    Boolean? disableGzipOutput
+    Boolean? disableRepeatResolution
+    File? dataset
+    Int? threads = 1
+    Int? memoryGb = 4
+    File? tmpDir
+    String? k
+    Float? covCutoff
+    Int? phredOffset
+
+    command {
+        set -e -o pipefail
+        ${preCommand}
+        spades.py \
+        ${"-o " + outputDir} \
+        ${true="--sc" false="" singleCell} \
+        ${true="--meta" false="" metagenomic} \
+        ${true="--rna" false="" rna} \
+        ${true="--plasmid" false="" plasmid} \
+        ${true="--iontorrent" false="" ionTorrent} \
+        ${"--12 " + interlacedReads }
+        ${"--threads " + threads } \
+        ${"-1 " + read1 } \
+        ${"-2 " + read2 } \
+        ${"-s " + singleRead } \
+        ${"--sanger " + sangerReads } \
+        ${"--pacbio " + pacbioReads } \
+        ${"--nanopore " + nanoporeReads } \
+        ${"--tslr " + tslrContigs } \
+        ${"--trusted-contigs " + trustedContigs } \
+        ${"--untrusted-contigs" + untrustedContigs } \
+        ${true="--only-error-correction" false="" onlyErrorCorrection } \
+        ${true="--only-assembler" false="" onlyAssembler } \
+        ${true="--careful" false="" careful } \
+        ${true="--disable-gzip-output" false="" disableGzipOutput} \
+        ${true="--disable-rr" false="" disableRepeatResolution } \
+        ${"--dataset " + dataset } \
+        ${"--threads " + threads } \
+        ${"--memory " + memoryGb } \
+        ${"-k " + k } \
+        ${"--cov-cutoff " + covCutoff } \
+        ${"--phred-offset " + phredOffset }
+    }
+    output {
+        Array[File] correctedReads = glob_wildcard(outputDir + "/corrected/*.fastq*")
+        File scaffolds = outputDir + "/scaffolds.fasta"
+        File contigs = outputDir + "/contigs.fasta"
+        File assemblyGraphGfa = outputDir + "/assembly_graph.gfa"
+        File assemblyGraphFastg = outputDir + "/assembly_graph.fastq"
+        File contigsPaths = outputDir + "/contigs.paths"
+        File scaffoldsPaths = outputDir + "/scaffolds.paths"
+        File params = outputDir + "/params.txt"
+        File log = outputDir + "/spades/log"
+    }
+    runtime {
+        cpu: select_first([threads])
+        memory: select_first([memoryGb]) + "G"
+    }
+}
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