From dabe9af06f6ad5c25b20f2836f0e8055b5e04ed9 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 3 May 2018 11:05:10 +0200
Subject: [PATCH] fix a few issues in spades
---
spades.wdl | 21 +++++++++++----------
1 file changed, 11 insertions(+), 10 deletions(-)
diff --git a/spades.wdl b/spades.wdl
index 49c095c..724285d 100644
--- a/spades.wdl
+++ b/spades.wdl
@@ -1,9 +1,8 @@
task spades {
String outputDir
String? preCommand
- File? read1
+ File read1
File? read2
- File? singleRead
File? interlacedReads
File? sangerReads
File? pacbioReads
@@ -22,12 +21,15 @@ task spades {
Boolean? disableGzipOutput
Boolean? disableRepeatResolution
File? dataset
- Int threads
- Int memoryGb
+ Int? threads
+ Int? memoryGb
File? tmpDir
String? k
Float? covCutoff
Int? phredOffset
+ Int finalThreads = select_first([threads,1])
+ Int totalMemory = select_first([memoryGb, finalThreads * 16])
+ Int clusterMemory = totalMemory / finalThreads
command {
set -e -o pipefail
@@ -40,9 +42,8 @@ task spades {
${true="--plasmid" false="" plasmid} \
${true="--iontorrent" false="" ionTorrent} \
${"--12 " + interlacedReads } \
- ${"-1 " + read1 } \
+ ${true="-1" false="-s" defined(read2)} ${read1} \
${"-2 " + read2 } \
- ${"-s " + singleRead } \
${"--sanger " + sangerReads } \
${"--pacbio " + pacbioReads } \
${"--nanopore " + nanoporeReads } \
@@ -55,8 +56,8 @@ task spades {
${true="--disable-gzip-output" false="" disableGzipOutput} \
${true="--disable-rr" false="" disableRepeatResolution } \
${"--dataset " + dataset } \
- ${"--threads " + threads } \
- ${"--memory " + memoryGb * threads } \
+ ${"--threads " + finalThreads} \
+ ${"--memory " + totalMemory } \
${"-k " + k } \
${"--cov-cutoff " + covCutoff } \
${"--phred-offset " + phredOffset }
@@ -73,7 +74,7 @@ task spades {
File log = outputDir + "/spades.log"
}
runtime {
- cpu: threads
- memory: memoryGb
+ cpu: finalThreads
+ memory: clusterMemory
}
}
\ No newline at end of file
--
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