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Commit 2bc6ec69 authored by Ruben Vorderman's avatar Ruben Vorderman
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complete unicycler

parent 87a75fe0
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2 merge requests!9Changes for virus assembly pipeline,!10Extra tasks required for assembly.
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unicycler.wdl
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...@@ -47,8 +47,8 @@ task unicycler { ...@@ -47,8 +47,8 @@ task unicycler {
mkdir -p ${out} mkdir -p ${out}
${preCommand} ${preCommand}
unicycler \ unicycler \
--short1 ${short1} \ ${"--short1 " + short1} \
--short2 ${short2} \ ${"--short2 " + short2} \
${"--unpaired " + unpaired} \ ${"--unpaired " + unpaired} \
${"--long " + long} \ ${"--long " + long} \
--out ${out} \ --out ${out} \
...@@ -88,7 +88,11 @@ task unicycler { ...@@ -88,7 +88,11 @@ task unicycler {
${"--scores " + scores } \ ${"--scores " + scores } \
${"--low_score " + lowScore } ${"--low_score " + lowScore }
} }
output {
File assemblyFasta = out + "/assembly.fasta"
File assemblyGfa = out + "/assembly.gfa"
File log = out + "/unicycler.log"
}
runtime { runtime {
cpu: threads cpu: threads
memory: memory memory: memory
......
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