Merge pull request #115 from biowdl/BIOWDL-253

Add bowtie

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

htseq.wdl

@@ -5,7 +5,7 @@ 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"

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 {