Merge pull request #147 from biowdl/bwakit

Add bwakit task

CHANGELOG.md

@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
 
 version 1.1.0-dev
 ---------------------------
++ Added bwakit task
 + Minimap2: Add the option for --MD tag
 + TALON: Update average memory needs for main TALON process
 

bwa.wdl

@@ -44,6 +44,99 @@ task Mem {
     }
 }
 
+task Kit {
+    input {
+        File read1
+        File? read2
+        BwaIndex bwaIndex
+        String outputPrefix
+        String? readgroup
+        Boolean sixtyFour = false
+
+        Int threads = 2
+        Int sortThreads = 2
+        Int memory = 10
+        String dockerImage = "biocontainers/bwakit:v0.7.15_cv1"
+    }
+
+    command {
+        set -e
+        bwa mem \
+          -t ~{threads} \
+          ~{"-R '" + readgroup}~{true="'" false="" defined(readgroup)} \
+          ~{bwaIndex.fastaFile} \
+          ~{read1} \
+          ~{read2} \
+          2> ~{outputPrefix}.log.bwamem | \
+        k8 /opt/conda/bin/bwa-postalt.js \
+          -p ~{outputPrefix}.hla \
+          ~{bwaIndex.fastaFile}~{true=".64.alt" false=".alt" sixtyFour} | \
+        samtools sort \
+          -@ ~{sortThreads} \
+          -m1G \
+          - \
+          -o ~{outputPrefix}.aln.bam
+        samtools index ~{outputPrefix}.aln.bam ~{outputPrefix}.aln.bai
+    }
+
+    output {
+        File outputBam = outputPrefix + ".aln.bam"
+        File outputBamIndex = outputPrefix + ".aln.bai"
+    }
+
+    runtime {
+        cpu: threads + sortThreads
+        memory: memory
+        docker: dockerImage
+    }
+
+    parameter_meta {
+        read1: {
+            description: "The first-end fastq file.",
+            category: "required"
+        }
+        read2: {
+            description: "The second-end fastq file.",
+            category: "common"
+        }
+        bwaIndex: {
+            description: "The BWA index, including a .alt file.",
+            category: "required"
+        }
+        outputPrefix: {
+            description: "The prefix of the output files, including any parent directories",
+            category: "required"
+        }
+        readgroup: {
+            description: "A readgroup identifier.",
+            category: "common"
+        }
+        sixtyFour: {
+            description: "Whether or not the index uses the '.64' suffixes.",
+            category: "common"
+        }
+        threads: {
+            description: "The number of threads to use for alignment.",
+            category: "advanced"
+        }
+        sortThreads: {
+            description: "The number of threads to use for sorting.",
+            category: "advanced"
+        }
+        memory: {
+            description: "The amount of memory this job will use.",
+            category: "advanced"
+        }
+        dockerImage: {
+            description: "The docker image used for this task. Changing this may result in errors which the developers may chose not to address.",
+            category: "advanced"
+        }
+
+        outputBam: "The produced BAM file."
+        outputBamIndex: "The index of the produced BAM file."
+    }
+}
+
 struct BwaIndex {
     File fastaFile
     Array[File] indexFiles