From 63c2d46b28126a8ab78f030a0f1c83c7525602c9 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 3 May 2018 11:09:42 +0200
Subject: [PATCH] fix unicycler memory
---
spades.wdl | 2 +-
unicycler.wdl | 12 +++++++-----
2 files changed, 8 insertions(+), 6 deletions(-)
diff --git a/spades.wdl b/spades.wdl
index 724285d..ce9de29 100644
--- a/spades.wdl
+++ b/spades.wdl
@@ -49,7 +49,7 @@ task spades {
${"--nanopore " + nanoporeReads } \
${"--tslr " + tslrContigs } \
${"--trusted-contigs " + trustedContigs } \
- ${"--untrusted-contigs" + untrustedContigs } \
+ ${"--untrusted-contigs " + untrustedContigs } \
${true="--only-error-correction" false="" onlyErrorCorrection } \
${true="--only-assembler" false="" onlyAssembler } \
${true="--careful" false="" careful } \
diff --git a/unicycler.wdl b/unicycler.wdl
index dac048a..f7aa36a 100644
--- a/unicycler.wdl
+++ b/unicycler.wdl
@@ -9,8 +9,10 @@ task unicycler {
Int? minFastaLength
Int? keep
Boolean? vcf
- Int threads
- Int memory
+ Int? threads
+ Int? memory
+ Int finalThreads = select_first(threads, 1)
+ Int finalMemory = select_first(memory, 4)
String? mode
Float? minBridgeQual
Int? linearSeqs
@@ -55,7 +57,7 @@ task unicycler {
${"--min_fasta_length " + minFastaLength} \
${"--keep " + keep } \
${true="--vcf" false="" vcf } \
- ${"--threads " + threads } \
+ ${"--threads " + finalThreads } \
${"--mode " + mode } \
${"--min_bridge_qual " + minBridgeQual } \
${"--linear_seqs " + linearSeqs } \
@@ -94,7 +96,7 @@ task unicycler {
File log = out + "/unicycler.log"
}
runtime {
- cpu: threads
- memory: memory
+ cpu: finalThreads
+ memory: finalMemory
}
}
\ No newline at end of file
--
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