From 47035fb2d2d414e0adc0517552fd151ff29f8b8b Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 8 Feb 2018 15:52:12 +0100
Subject: [PATCH] added bwa index task
---
bwa.wdl | 32 +++++++++++++++++++++++++++++++-
1 file changed, 31 insertions(+), 1 deletion(-)
diff --git a/bwa.wdl b/bwa.wdl
index daba87b..a0f228e 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -81,7 +81,7 @@ task mem {
${"-I " + I } \
${referenceFile} ${read1} ${read2} \
| picard SortSam CREATE_INDEX=TRUE TMP_DIR=null \
- INPUT=/dev/stdin OUTPUT=${outputFile}
+ INPUT=/dev/stdin SORT_ORDER=coordinate OUTPUT=${outputFile}
}
output {
File alignedFile = select_first([outputFile])
@@ -90,4 +90,34 @@ task mem {
cpu: select_first([threads])
memory: select_first([memory])
}
+}
+
+task index {
+ File fasta
+ String? preCommand
+ String? constructionAlgorithm
+ Int? blockSize
+ String? outputDir
+ String fastaFilename = basename(fasta)
+
+ command {
+ set -e -o pipefail
+ ${"mkdir -p " + outputDir}
+ ${preCommand}
+ ln -sf ${fasta} ${outputDir + "/"}${fastaFilename}
+ bwa index \
+ ${"-a " + constructionAlgorithm} \
+ ${"-b" + blockSize} \
+ ${outputDir + "/"}${fastaFilename}
+ }
+
+ output {
+ File indexedFasta = if (defined(outputDir)) then select_first([outputDir]) + "/" + fastaFilename else fastaFilename
+ }
+ parameter_meta {
+ fasta: "Fasta file to be indexed"
+ constructionAlgorithm: "-a STR BWT construction algorithm: bwtsw, is or rb2 [auto]"
+ blockSize: "-b INT block size for the bwtsw algorithm (effective with -a bwtsw) [10000000]"
+ outputDir: "index will be created in this output directory"
+ }
}
\ No newline at end of file
--
GitLab