From 8df9a800fb56341a2c0b964f9300d49394cf485d Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Wed, 28 Oct 2020 06:52:29 +0100
Subject: [PATCH] Update to CCS version 5
---
ccs.wdl | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
diff --git a/ccs.wdl b/ccs.wdl
index 60e4371..bcebefe 100644
--- a/ccs.wdl
+++ b/ccs.wdl
@@ -29,12 +29,14 @@ task CCS {
Float minReadQuality = 0.99
String logLevel = "WARN"
File subreadsFile
+ File? subreadsIndexFile
+ String? chunkString
String outputPrefix
Int cores = 2
String memory = "2G"
Int timeMinutes = 1440
- String dockerImage = "quay.io/biocontainers/pbccs:4.2.0--0"
+ String dockerImage = "quay.io/biocontainers/pbccs:5.0.0--0"
}
command {
@@ -48,7 +50,8 @@ task CCS {
--min-rq ~{minReadQuality} \
--log-level ~{logLevel} \
--num-threads ~{cores} \
- ~{"--report-file " + outputPrefix + ".ccs.report.txt"} \
+ ~{"--chunk " + chunkString} \
+ ~{"--report-json " + outputPrefix + ".ccs.report.json"} \
~{"--log-file " + outputPrefix + ".ccs.stderr.log"} \
~{subreadsFile} \
~{outputPrefix + ".ccs.bam"}
@@ -57,7 +60,7 @@ task CCS {
output {
File ccsBam = outputPrefix + ".ccs.bam"
File ccsBamIndex = outputPrefix + ".ccs.bam.pbi"
- File ccsReport = outputPrefix + ".ccs.report.txt"
+ File ccsReport = outputPrefix + ".ccs.report.json"
File ccsStderr = outputPrefix + ".ccs.stderr.log"
}
@@ -77,6 +80,9 @@ task CCS {
minReadQuality: {description: "Minimum predicted accuracy in [0, 1].", category: "common"}
logLevel: {description: "Set log level. Valid choices: (TRACE, DEBUG, INFO, WARN, FATAL).", category: "advanced"}
subreadsFile: {description: "Subreads input file.", category: "required"}
+ subreadsIndexFile: {description: "Index for the subreads input file.", category: "required"}
+ outputPrefix: {description: "Output directory path + output file prefix.", category: "advanced"}
+ chunkString: {descpription: "Chunk string (e.g. 1/4, 5/5) for CCS.", category: "advanced"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
cores: {description: "The number of cores to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
--
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