Add cwl and docker files

[lightning.git] / cwl / lightning / lightning-choose-samples.cwl

diff --git a/cwl/lightning/lightning-choose-samples.cwl b/cwl/lightning/lightning-choose-samples.cwl
new file mode 100644 (file)
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+++ b/cwl/lightning/lightning-choose-samples.cwl
@@ -0,0 +1,53 @@
+# Copyright (C) The Lightning Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+  NetworkAccess:
+    networkAccess: true
+hints:
+  DockerRequirement:
+    dockerPull: lightning
+  ResourceRequirement:
+    coresMin: 2
+    ramMin: 10000
+  arv:RuntimeConstraints:
+    keep_cache: 20000
+    outputDirType: keep_output_dir
+inputs:
+  matchgenome: string
+  libdir: Directory
+  phenotypesdir: Directory
+  trainingsetsize: float
+  randomseed: int
+outputs:
+  samplescsv:
+    type: File
+    outputBinding:
+      glob: "samples.csv"
+baseCommand: [lightning, choose-samples]
+arguments:
+  - "-local=true"
+  - prefix: "-input-dir="
+    valueFrom: $(inputs.libdir)
+    separate: false
+  - prefix: "-output-dir="
+    valueFrom: $(runtime.outdir)
+    separate: false
+  - prefix: "-match-genome="
+    valueFrom: $(inputs.matchgenome)
+    separate: false
+  - prefix: "-case-control-file="
+    valueFrom: $(inputs.phenotypesdir)
+    separate: false
+  - "-case-control-column=AD"
+  - prefix: "-training-set-size="
+    valueFrom: $(inputs.trainingsetsize)
+    separate: false
+  - prefix: "-random-seed="
+    valueFrom: $(inputs.randomseed)
+    separate: false