expose read_utils.py::fastq_to_bam in wdl task and workflow

pipes/WDL/workflows/fastq_to_bam.wdl

@@ -0,0 +1,5 @@
+import "tasks_read_utils.wdl" as read_utils
+
+workflow paired_fastqs_to_bam {
+    call read_utils.fastq_to_bam
+}

pipes/WDL/workflows/tasks/tasks_read_utils.wdl

@@ -37,4 +37,33 @@ task downsample_bams {
   }
 }
 
+task fastq_to_bam {
+  File  in_fastq1
+  File  in_fastq2
+  File? header
 
+  # also used for outfile name
+  String? sample_name = basename(basename(basename(basename(basename(basename(in_fastq1, ".1.fastq"),".1.fq"),".fastq"),".fq"),".fq1"),".fastq1")
+
+  command {
+    read_utils.py fastq_to_bam \
+        ${in_fastq1} \
+        ${in_fastq2} \
+        ${sample_name}.bam \
+        ${'--sampleName=' + sample_name} \
+        ${'--header ' + header} \
+        --JVMmemory "1g"
+  }
+
+  output {
+    File out_bam            = "${sample_name}.bam"
+    String viralngs_version = "viral-ngs_version_unknown"
+  }
+  runtime {
+    docker: "quay.io/broadinstitute/viral-ngs"
+    memory: "3 GB"
+    cpu: 2
+    dx_instance_type: "mem1_ssd1_v2_x4"
+    preemptible: 0
+  }
+}