Skip to content
Snippets Groups Projects
Commit d604025c authored by Ruben Vorderman's avatar Ruben Vorderman
Browse files

Fix bwakit command

parent 2aa28e29
No related branches found
No related tags found
No related merge requests found
......@@ -100,7 +100,7 @@ task Kit {
# BWA needs slightly more memory than the size of the index files (~10%). Add a margin for safety here.
Int memoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G") * 1.2) + sortMemoryPerThreadGb * sortThreads
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 220 / threads)
# Contains bwa 0.7.17 bwakit 0.7.17.dev1 and samtools
# Contains bwa 0.7.17 bwakit 0.7.17.dev1 and samtools 1.10
String dockerImage = "quay.io/biocontainers/mulled-v2-ad317f19f5881324e963f6a6d464d696a2825ab6:c59b7a73c87a9fe81737d5d628e10a3b5807f453-0"
}
......@@ -114,7 +114,7 @@ task Kit {
~{read1} \
~{read2} \
2> ~{outputPrefix}.log.bwamem | \
k8 /opt/conda/bin/bwa-postalt.js \
bwa-postalt.js \
-p ~{outputPrefix}.hla \
~{bwaIndex.fastaFile}~{true=".64.alt" false=".alt" sixtyFour} | \
samtools sort \
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment