Move workflows into main repo

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

1 files changed, 32 insertions, 0 deletions

diff --git a/workflows/pangenome-generate/seqkit-rmdup.cwl b/workflows/pangenome-generate/seqkit-rmdup.cwl
new file mode 100644
index 0000000..d3626f5
--- /dev/null
+++ b/workflows/pangenome-generate/seqkit-rmdup.cwl
@@ -0,0 +1,32 @@
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+  readsFA: File[]
+outputs:
+  readsMergeDedup:
+    type: File
+    outputBinding:
+      glob: readsMergeDedup.fasta
+requirements:
+  InlineJavascriptRequirement: {}
+hints:
+  DockerRequirement:
+    dockerPull: "quay.io/biocontainers/seqkit:0.7.1--0"
+  ResourceRequirement:
+    coresMin: 8
+    coresMax: 32
+    ramMin: $(7 * 1024)
+    outdirMin: |
+      ${
+        var sum = 0;
+        for (var i = 0; i < inputs.readsFA.length; i++) {
+          sum += inputs.readsFA[i].size;
+        }
+        return (sum/(1024*1024*1024)+1) + 20;
+      }
+baseCommand: seqkit
+arguments: [rmdup,
+            --by-seq,
+            --ignore-case,
+            -o, readsMergeDedup.fasta,
+            $(inputs.readsFA)]