From b3545b27947b9221f9f5e30d55c70f2284d5d7cc Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 4 May 2018 11:31:34 +0200
Subject: [PATCH] add fastq task
---
samtools.wdl | 47 +++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 47 insertions(+)
diff --git a/samtools.wdl b/samtools.wdl
index 249143f..f425d2e 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -65,3 +65,50 @@ task Flagstat {
File flagstat = outputPath
}
}
+
+task fastq {
+ String? preCommand
+ File inputBam
+ String outputRead1
+ String? outputRead2
+ String? outputRead0
+ Int? includeFilter
+ Int? excludeFilter
+ Int? excludeSpecificFilter
+ Boolean? appendReadNumber
+ Boolean? outputQuality
+ Int? compressionLevel
+ Int? threads
+ Int? memory
+ Int totalThreads = select_first([threads, 1])
+
+ command {
+ ${preCommand}
+ samtools fastq \
+ ${true="-1" false="-s" defined(outputRead2)} ${outputRead1} \
+ ${"-2 " + outputRead2} \
+ ${"-0 " + outputRead0} \
+ ${"-f " + includeFilter} \
+ ${"-F " + excludeFilter} \
+ ${"-G " + excludeSpecificFilter} \
+ ${true="-N" false="-n" appendReadNumber} \
+ ${true="-O" false="" outputQuality} \
+ ${"-c " + compressionLevel} \
+ ${"--threads " + totalThreads} \
+
+ }
+ runtime {
+ cpu: totalThreads
+ memory: select_first([memory, 1])
+ }
+ parameter_meta {
+ preCommand: "A command that is run before the task. Can be used to activate environments"
+ inputBam: "The bam file to process."
+ outputRead1: "If only outputRead1 is given '-s' flag is assumed. Else '-1'."
+ includeFilter: "Include reads with ALL of these flags. Corresponds to '-f'"
+ excludeFilter: "Exclude reads with ONE OR MORE of these flags. Corresponds to '-F'"
+ excludeSpecificFilter: "Exclude reads with ALL of these flags. Corresponds to '-G'"
+ appendReadNumber: "Append /1 and /2 to the read name, or don't. Corresponds to '-n/N"
+
+ }
+}
--
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