Merge branch 'develop' into BIOWDL-253

biopet/biopet.wdl

@@ -84,7 +84,7 @@ task ExtractAdaptersFastqc {
         Float? adapterCutoff
         Boolean? outputAsFasta
 
-        Int memory = 4
+        Int memory = 8
         Float memoryMultiplier = 5 # This is ridiculous...
         String dockerTag = "0.2--1"
     }
@@ -179,7 +179,7 @@ task FastqSync {
     output {
         FastqPair out1 = object {
           R1: out1path,
-          R1: out2path
+          R2: out2path
         }
     }
     

collect-columns.wdl

@@ -13,7 +13,7 @@ task CollectColumns {
         File? referenceGtf
         String? featureAttribute
 
-        String dockerTag = "0.1.1--py_0"
+        String dockerTag = "0.2.0--py_1"
     }
 
     command {

common.wdl

@@ -131,23 +131,6 @@ task MapMd5 {
     }
 }
 
-task ObjectMd5 {
-    input {
-        Object the_object
-    }
-
-    command {
-        cat ~{write_object(the_object)} |  md5sum - | sed -e 's/  -//'
-    }
-
-    output {
-        String md5sum = read_string(stdout())
-    }
-
-    runtime {
-        memory: 1
-    }
-}
 
 task StringArrayMd5 {
     input {

cutadapt.wdl

@@ -62,7 +62,7 @@ task Cutadapt {
         String? reportPath
 
         Int cores = 1
-        Int memory = 8
+        Int memory = 16
         String dockerTag = "2.3--py36h14c3975_0"
     }
 

hisat2.wdl

@@ -2,8 +2,7 @@ version 1.0
 
 task Hisat2 {
     input {
-        File indexDirectory
-        String indexBasename
+        Array[File]+ indexFiles
         File inputR1
         File? inputR2
         String outputBam
@@ -24,7 +23,7 @@ task Hisat2 {
         mkdir -p $(dirname ~{outputBam})
         hisat2 \
         -p ~{threads} \
-        -x ~{indexDirectory}/~{indexBasename} \
+        -x ~{sub(indexFiles[0], "\.[0-9]\.ht2", "")} \
         ~{true="-1" false="-U" defined(inputR2)} ~{inputR1} \
         ~{"-2" + inputR2} \
         --rg-id ~{readgroup} \

htseq.wdl

@@ -10,7 +10,7 @@ task HTSeqCount {
         String order = "pos"
         String stranded = "no"
 
-        Int memory = 20
+        Int memory = 40
         String dockerTag = "0.9.1--py36h7eb728f_2"
     }
 

mergecounts.wdl

 version 1.0
 
+#DEPRECATED
 task MergeCounts {
     input {
         Array[File] inputFiles

picard.wdl

@@ -50,8 +50,8 @@ task CollectMultipleMetrics {
         Boolean collectSequencingArtifactMetrics = true
         Boolean collectQualityYieldMetrics = true
 
-        Int memory = 4
-        Float memoryMultiplier = 3.5
+        Int memory = 8
+        Float memoryMultiplier = 4
         String dockerTag = "8dde04faba6c9ac93fae7e846af3bafd2c331b3b-0"
     }
 
@@ -133,8 +133,8 @@ task CollectRnaSeqMetrics {
         String basename
         String strandSpecificity = "NONE"
 
-        Int memory = 4
-        Float memoryMultiplier = 3.0
+        Int memory = 8
+        Float memoryMultiplier = 4.0
         String dockerTag = "8dde04faba6c9ac93fae7e846af3bafd2c331b3b-0"
     }
 
@@ -278,7 +278,7 @@ task MarkDuplicates {
         String outputBamPath
         String metricsPath
 
-        Int memory = 4
+        Int memory = 8
         Float memoryMultiplier = 3.0
         String dockerTag = "2.18.26--0"
 

star.wdl

@@ -2,14 +2,14 @@ version 1.0
 
 task Star {
     input {
-        Array[File] inputR1
+        Array[File]+ inputR1
         Array[File]? inputR2
-        File genomeDir
+        Array[File]+ indexFiles
         String outFileNamePrefix
         String outSAMtype = "BAM SortedByCoordinate"
         String readFilesCommand = "zcat"
         String? outStd
-        String? twopassMode
+        String? twopassMode = "Basic"
         Array[String]? outSAMattrRGline
         String? outSAMunmapped = "Within KeepPairs"
         Int? limitBAMsortRAM
@@ -19,7 +19,7 @@ task Star {
         String dockerTag = "2.6.0c--0"
     }
 
-    # Needs to be extended for all possible output extensions
+    #TODO Needs to be extended for all possible output extensions
     Map[String, String] samOutputNames = {"BAM SortedByCoordinate": "sortedByCoord.out.bam"}
 
     command {
@@ -28,7 +28,7 @@ task Star {
         STAR \
         --readFilesIn ~{sep=',' inputR1} ~{sep="," inputR2} \
         --outFileNamePrefix ~{outFileNamePrefix} \
-        --genomeDir ~{genomeDir} \
+        --genomeDir ~{sub(indexFiles[0], basename(indexFiles[0]), "")} \
         --outSAMtype ~{outSAMtype} \
         --readFilesCommand ~{readFilesCommand} \
         ~{"--outSAMunmapped " + outSAMunmapped} \