1 files changed, 23 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/minimap2.cwl b/workflows/pangenome-generate/minimap2.cwl
new file mode 100644
index 0000000..bf19ef7
--- /dev/null
+++ b/workflows/pangenome-generate/minimap2.cwl
@@ -0,0 +1,23 @@
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+  readsFA: File
+outputs:
+  readsPAF: stdout
+requirements:
+  InlineJavascriptRequirement: {}
+hints:
+  DockerRequirement:
+    dockerPull: "quay.io/biocontainers/minimap2:2.17--h8b12597_1"
+  ResourceRequirement:
+    coresMin: 8
+    coresMax: 32
+    ramMin: $(7 * 1024)
+    outdirMin: $(Math.ceil(inputs.readsFA.size/(1024*1024*1024) + 20))
+stdout: $(inputs.readsFA.nameroot).paf
+baseCommand: minimap2
+arguments: [-cx, asm20,
+            -w, "1",
+            -t, $(runtime.cores),
+            $(inputs.readsFA),
+            $(inputs.readsFA)]