added spoa workflow in a low memory consumption mode

1 files changed, 27 insertions, 0 deletions

diff --git a/workflows/pangenome-generate/spoa.cwl b/workflows/pangenome-generate/spoa.cwl
new file mode 100644
index 0000000..1e390d8
--- /dev/null
+++ b/workflows/pangenome-generate/spoa.cwl
@@ -0,0 +1,27 @@
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+  readsFA: File
+stdout: $(inputs.readsFA.nameroot).g6.gfa
+script:
+    type: File
+    default: {class: File, location: relabel-seqs.py}
+outputs:
+  spoaGFA:
+    type: stdout
+requirements:
+  InlineJavascriptRequirement: {}
+  ShellCommandRequirement: {}
+hints:
+  DockerRequirement:
+    dockerPull: "quay.io/biocontainers/spoa:3.0.2--hc9558a2_0"
+  ResourceRequirement:
+    coresMin: 1
+    ramMin: $(15 * 1024)
+    outdirMin: $(Math.ceil(inputs.readsFA.size/(1024*1024*1024) + 20))
+baseCommand: spoa
+arguments: [
+    $(inputs.readsFA),
+    -G,
+    -g, '-6'
+]