Add the Common Workflow Language standard (#3902)

* Add the language for the Common Workflow Language standards

* add CWL grammer

* add MIT licensed CWL sample

* script/set-language-ids --update for CWL

samples/Common Workflow Language/trunk-peak-score.cwl

@@ -0,0 +1,36 @@
+#!/usr/bin/env cwl-runner
+# Originally from
+# https://github.com/Duke-GCB/GGR-cwl/blob/54e897263a702ff1074c8ac814b4bf7205d140dd/utils/trunk-peak-score.cwl
+# Released under the MIT License:
+# https://github.com/Duke-GCB/GGR-cwl/blob/54e897263a702ff1074c8ac814b4bf7205d140dd/LICENSE
+# Converted to CWL v1.0 syntax using
+# https://github.com/common-workflow-language/cwl-upgrader
+# and polished by Michael R. Crusoe <mrc@commonwl.org>
+# All modifications also released under the MIT License
+cwlVersion: v1.0
+class: CommandLineTool
+doc: Trunk scores in ENCODE bed6+4 files
+
+hints:
+  DockerRequirement:
+    dockerPull: dukegcb/workflow-utils
+
+inputs:
+  peaks:
+    type: File
+  sep:
+    type: string
+    default: \t
+
+outputs:
+  trunked_scores_peaks:
+    type: stdout
+
+baseCommand: awk
+
+arguments:
+- -F $(inputs.sep)
+- BEGIN{OFS=FS}$5>1000{$5=1000}{print}
+- $(inputs.peaks.path)
+
+stdout: $(inputs.peaks.nameroot).trunked_scores$(inputs.peaks.nameext)