1 files changed, 29 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/odgi-build-from-xpoa-gfa.cwl b/workflows/pangenome-generate/odgi-build-from-xpoa-gfa.cwl
new file mode 100644
index 0000000..eee4031
--- /dev/null
+++ b/workflows/pangenome-generate/odgi-build-from-xpoa-gfa.cwl
@@ -0,0 +1,29 @@
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+  inputGFA: File
+outputs:
+  odgiGraph:
+    type: File
+    outputBinding:
+      glob: $(inputs.inputGFA.nameroot).unchop.sorted.odgi
+requirements:
+  InlineJavascriptRequirement: {}
+hints:
+  DockerRequirement:
+    dockerPull: "odgi-bash-binutils:latest"
+  ResourceRequirement:
+    coresMin: 4
+    ramMin: $(15 * 1024)
+    outdirMin: $(Math.ceil((inputs.inputGFA.size/(1024*1024*1024)+1) * 2))
+  InitialWorkDirRequirement:
+    # Will fail if input file is not writable (odgi bug)
+    listing:
+      - entry: $(inputs.inputGFA)
+        writable: true
+arguments:
+  - "sh"
+  - "-c"
+  - >-
+    odgi build -g '$(inputs.inputGFA.path)' -o - | odgi unchop -i - -o - |
+    odgi sort -i - -p s -o $(inputs.inputGFA.nameroot).unchop.sorted.odgi