From dddc35b2da205e56c44b413b569d8c2abd99e018 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Jan 2018 15:40:51 +0100
Subject: [PATCH] add spades task
---
spades.wdl | 80 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 80 insertions(+)
create mode 100644 spades.wdl
diff --git a/spades.wdl b/spades.wdl
new file mode 100644
index 0000000..fd9b4ed
--- /dev/null
+++ b/spades.wdl
@@ -0,0 +1,80 @@
+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"
+ }
+}
\ No newline at end of file
--
GitLab