Merge pull request #258 from biowdl/ccs5

Update to CCS version 5

CHANGELOG.md

@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
 
 version 5.0.0-dev
 ---------------------------
++ CCS: Update CCS to version 5.
 + deepvariant: Add task for DeepVariant.
 + gatk: Make intervals optional for GenotypeGVCFs.
 + isoseq3: Add required bam index input to isoseq3.

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 +80,8 @@ 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, required when using chunkString.", 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"}