Adding wdl to get bedgraphs with coverage

bamtobedwithcoverage.wdl

@@ -0,0 +1,91 @@
+version 1.0
+
+workflow bamtobigwig {
+
+    input {
+        File genome
+        File fastq
+    }
+
+    call minimapalign {
+        input:
+            fastq = fastq,
+            genome = genome
+    }
+    call filter {
+        input:
+            sortedbam = minimapalign.sortedbam
+    }
+    call tobedgraph {
+        input:
+            genome = genome,
+            filteredbai = filter.filteredbai,
+            filteredbam = filter.filteredbam
+    }
+    output {
+        File FivemCcpgbedgraph = tobedgraph.FivemCcpgbedgraph
+    }
+
+    meta {
+        author: "Martin Aryee"
+        email:"[email protected]"
+    }
+}
+task minimapalign {
+    input {
+        File fastq
+        File genome
+    }
+    command <<<
+    samtools import -T "*" ~{fastq} > temp.bam
+    samtools fastq -T "*" temp.bam | minimap2 -ax map-ont -y ~{genome} - | samtools sort -T tmp -o sorted.bam
+    samtools index sorted.bam
+    >>>
+    runtime {
+        docker: "us-central1-docker.pkg.dev/aryeelab/docker/minimap2:latest"
+		memory: "64G"
+		disks: "local-disk 500 SSD"
+		cpu: 8
+    }
+    output {
+        File sortedbam = "sorted.bam"
+    }
+}
+task filter {
+    input {
+        File sortedbam
+    }
+    command <<<
+    samtools view -bh -q 50 ~{sortedbam} > filtered.bam
+    samtools index filtered.bam
+    >>>
+    runtime {
+        docker: "us-central1-docker.pkg.dev/aryeelab/docker/samtools:latest"
+		memory: "64G"
+		disks: "local-disk 500 SSD"
+		cpu: 8
+    }
+    output {
+        File filteredbam = "filtered.bam"
+        File filteredbai = "filtered.bam.bai"
+    }
+}
+task tobedgraph {
+    input {
+        File genome
+        File filteredbam
+        File filteredbai
+    }
+    command <<<
+    modkit pileup ~{filteredbam} big_5mc.bed --cpg --ref ~{genome} --combine-strands --ignore h --bedgraph
+    >>>
+    runtime {
+        docker: "us-central1-docker.pkg.dev/aryeelab/docker/modkit:latest"
+		memory: "64G"
+		disks: "local-disk 500 SSD"
+		cpu: 8
+    }
+    output {
+        File FivemCcpgbedgraph = "5mC.cpg.bedgraph"
+    }
+}