From a5d696686cb496a0a2bc60c74dda1f52490d44c1 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 4 May 2018 13:31:07 +0200
Subject: [PATCH] added bwa index and samtools fastq
---
bwa.wdl | 34 ++++++++++++++++++++++++++++++++++
samtools.wdl | 5 +++++
2 files changed, 39 insertions(+)
diff --git a/bwa.wdl b/bwa.wdl
index 0a8b37f..5839a9c 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -3,6 +3,7 @@ task BwaMem {
File inputR1
File? inputR2
String referenceFasta
+ Array[File] indexFiles # These indexFiles need to be added, otherwise cromwell will not find them.
String outputPath
String? readgroup
@@ -26,3 +27,36 @@ task BwaMem {
memory: if defined(memory) then memory else 8
}
}
+
+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 indexBase = if (defined(outputDir)) then select_first([outputDir]) + "/" + fastaFilename else fastaFilename
+ File indexedFasta = indexBase
+ Array[File] indexFiles = [indexBase + ".bwt",indexBase + ".pac",indexBase + ".sa",indexBase + ".amb",indexBase + ".ann"]
+ }
+ 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"
+ }
+}
+
diff --git a/samtools.wdl b/samtools.wdl
index f425d2e..c9207d3 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -97,6 +97,11 @@ task fastq {
${"--threads " + totalThreads} \
}
+ output {
+ File read1 = outputRead1
+ File? read2 = outputRead2
+ File? read0 = outputRead0
+ }
runtime {
cpu: totalThreads
memory: select_first([memory, 1])
--
GitLab