1 files changed, 29 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/seqwish.cwl b/workflows/pangenome-generate/seqwish.cwl
new file mode 100644
index 0000000..9f8cb15
--- /dev/null
+++ b/workflows/pangenome-generate/seqwish.cwl
@@ -0,0 +1,29 @@
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+  readsFA: File
+  readsPAF: File
+  kmerSize:
+    type: int
+    default: 16
+outputs:
+  seqwishGFA:
+    type: File
+    outputBinding:
+      glob: $(inputs.readsPAF.nameroot).gfa
+requirements:
+  InlineJavascriptRequirement: {}
+hints:
+  DockerRequirement:
+    dockerPull: "quay.io/biocontainers/seqwish:0.4.1--h8b12597_0"
+  ResourceRequirement:
+    coresMin: 4
+    ramMin: $(7 * 1024)
+    outdirMin: $(Math.ceil(inputs.readsFA.size/(1024*1024*1024) + 20))
+stdout: $(inputs.readsFA.nameroot).paf
+baseCommand: seqwish
+arguments: [-t, $(runtime.cores),
+            -k, $(inputs.kmerSize),
+            -s, $(inputs.readsFA),
+            -p, $(inputs.readsPAF),
+            -g, $(inputs.readsPAF.nameroot).gfa]