From f91f5982f82c12b331145a89856308c67a80b3fb Mon Sep 17 00:00:00 2001
From: pjvan_thof <pjrvanthof@gmail.com>
Date: Thu, 1 Mar 2018 14:27:49 +0100
Subject: [PATCH] Adding alignment step
---
bwa.wdl | 18 ++++++++++++++++++
fastqc.wdl | 10 +---------
samtools.wdl | 24 ++++++++++++++++++++++++
3 files changed, 43 insertions(+), 9 deletions(-)
create mode 100644 bwa.wdl
create mode 100644 samtools.wdl
diff --git a/bwa.wdl b/bwa.wdl
new file mode 100644
index 0000000..e5bac65
--- /dev/null
+++ b/bwa.wdl
@@ -0,0 +1,18 @@
+task BwaMem {
+ File inputR1
+ File? inputR2
+ String referenceFasta
+ String outputPath
+ String? readgroup
+
+ command {
+ set -e -o pipefail
+ mkdir -p $(dirname ${outputPath})
+ bwa mem ${"-R '" + readgroup + "'"} \
+ ${referenceFasta} ${inputR1} ${inputR2} | samtools sort --output-fmt BAM - > ${outputPath}
+ }
+
+ output {
+ File bamFile = outputPath
+ }
+}
diff --git a/fastqc.wdl b/fastqc.wdl
index 657c792..d5cd520 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -48,15 +48,7 @@ task fastqc {
File rawReport = reportDir + "/fastqc_data.txt"
File htmlReport = reportDir + "/fastqc_report.html"
File summary = reportDir + "/summary.txt"
- File adapterContent = reportDir + "/Images/adapter_content.png"
- File duplicationLevels = reportDir + "/Images/duplication_levels.png"
- File perBaseNContent = reportDir + "/Images/per_base_n_content.png"
- File perBaseQuality = reportDir + "/Images/per_base_quality.png"
- File perBaseSequenceContent = reportDir + "/Images/per_base_sequence_content.png"
- File perSequenceGCContent = reportDir + "/Images/per_sequence_gc_content.png"
- File perSequenceQuality = reportDir + "/Images/per_sequence_quality.png"
- File perTileQuality = reportDir + "/Images/per_tile_quality.png"
- File sequenceLengthDistribution = reportDir + "/Images/sequence_length_distribution.png"
+ Array[File] images = glob(outdirPath + "/*/Images/*.png")
}
runtime {
diff --git a/samtools.wdl b/samtools.wdl
new file mode 100644
index 0000000..6fee4d0
--- /dev/null
+++ b/samtools.wdl
@@ -0,0 +1,24 @@
+task SamtoolsIndex {
+ String bamFilePath
+
+ command {
+ samtools index ${bamFilePath}
+ }
+
+ output {
+ File indexFile = bamFilePath + ".bai"
+ }
+}
+
+task SamtoolsMerge {
+ Array[File] bamFiles
+ String outputBamPath
+
+ command {
+ samtools merge ${outputBamPath} ${bamFiles}
+ }
+
+ output {
+ File bamFile = outputBamPath
+ }
+}
\ No newline at end of file
--
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