Merge branch 'develop' into KG-295

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
         }
     }
     

bowtie.wdl

+version 1.0
+
+# MIT License
+#
+# Copyright (c) 2018 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task Bowtie {
+    input {
+        Array[File]+ readsUpstream
+        Array[File]+? readsDownstream
+        String outputPath = "mapped.bam"
+        Array[File]+ indexFiles
+        Int? seedmms
+        Int? seedlen
+        Int? k
+        Boolean best = false
+        Boolean strata = false
+        String? samRG
+        Int threads = 1
+        Int memory = 8
+        Int picardMemory = 4
+        # Image contains bowtie=1.2.2 and picard=2.9.2
+        String dockerImage = "quay.io/biocontainers/mulled-v2-bfe71839265127576d3cd749c056e7b168308d56:1d8bec77b352cdcf3e9ff3d20af238b33ed96eae-0"
+    }
+
+    # Assume fastq input with -q flag.
+    # The output always needs to be SAM as it is piped into Picard SortSam
+    # Hence, the --sam flag is used.
+
+    command {
+        set -e -o pipefail
+        mkdir -p $(dirname ~{outputPath})
+        bowtie -q \
+        --sam \
+        ~{"--seedmms " +  seedmms} \
+        ~{"--seedlen " + seedlen} \
+        ~{"-k " + k} \
+        ~{true="--best" false="" best} \
+        ~{true="--strata" false="" strata} \
+        ~{"--threads " + threads} \
+        ~{"--sam-RG '" + samRG}~{true="'" false="" defined(samRG)} \
+        ~{sub(indexFiles[0], "(\.rev)?\.[0-9]\.ebwt$", "")} \
+        ~{true="-1" false="" defined(readsDownstream)} ~{sep="," readsUpstream} \
+        ~{true="-2" false="" defined(readsDownstream)} ~{sep="," readsDownstream} \
+        | picard -Xmx~{picardMemory}G SortSam \
+        INPUT=/dev/stdin \
+        OUTPUT=~{outputPath} \
+        SORT_ORDER=coordinate \
+        CREATE_INDEX=true
+    }
+
+    output {
+        File outputBam = outputPath
+        File outputBamIndex = sub(outputPath, "\.bam$", ".bai")
+    }
+
+    runtime {
+        cpu: threads
+        memory: memory + picardMemory + picardMemory
+        docker: dockerImage
+    }
+}
+
+struct BowtieIndex {
+    File fasta
+    Array[File] indexFiles
+}
\ No newline at end of file

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

@@ -5,12 +5,12 @@ task HTSeqCount {
         Array[File]+ inputBams
         Array[File]+ inputBamsIndex
         File gtfFile
-        String outputTable
+        String outputTable = "output.tsv"
         String format = "bam"
         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

multiqc.wdl

@@ -5,7 +5,7 @@ task MultiQC {
         String dockerTag = "1.7--py_1"
         # Use a string here so cromwell does not relocate an entire analysis directory
         String analysisDirectory
-        Array[File] dependencies   # This must be used in order to run multiqc after these tasks.
+        Array[File] dependencies = []  # This must be used in order to run multiqc after these tasks.
         Boolean force = false
         Boolean dirs = false
         Int? dirsDepth
@@ -37,6 +37,7 @@ task MultiQC {
         String? clConfig
         Boolean verbose  = false
         Boolean quiet = false
+        Array[Boolean] finished = []  # An array of booleans that can be used to let multiqc wait on stuff.
     }
 
     command {

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} \