Merge pull request #654 from common-workflow-language/hashbang

mr-c · web-flow · commit 1dd77623d90c · 2018-02-11T18:39:38.000+01:00
make executable nearly all CWL descriptions in this repo
diff --git a/appveyor.yml b/appveyor.yml
@@ -31,6 +31,7 @@ install:
   - "python -c \"import struct; print(struct.calcsize('P') * 8)\""
 
 build_script:
+  - "%CMD_IN_ENV% pip install -U setuptools pip"
   - "%CMD_IN_ENV% pip install ."
 
 
diff --git a/tests/checker_wf/broken-wf.cwl b/tests/checker_wf/broken-wf.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: Workflow
 cwlVersion: v1.0
 requirements:
diff --git a/tests/checker_wf/broken-wf2.cwl b/tests/checker_wf/broken-wf2.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: Workflow
 cwlVersion: v1.0
 requirements:
diff --git a/tests/checker_wf/cat.cwl b/tests/checker_wf/cat.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: cat
diff --git a/tests/checker_wf/echo.cwl b/tests/checker_wf/echo.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: echo
diff --git a/tests/checker_wf/functional-wf.cwl b/tests/checker_wf/functional-wf.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: Workflow
 cwlVersion: v1.0
 requirements:
diff --git a/tests/echo.cwl b/tests/echo.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 inputs:
diff --git a/tests/override/echo-wf.cwl b/tests/override/echo-wf.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: Workflow
 inputs:
diff --git a/tests/override/echo.cwl b/tests/override/echo.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 requirements:
diff --git a/tests/random_lines.cwl b/tests/random_lines.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 id: "random_lines"
diff --git a/tests/random_lines_mapping.cwl b/tests/random_lines_mapping.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 id: "random_lines"
diff --git a/tests/seqtk_seq.cwl b/tests/seqtk_seq.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 id: "seqtk_seq"
diff --git a/tests/seqtk_seq_with_docker.cwl b/tests/seqtk_seq_with_docker.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 id: "seqtk_seq"
diff --git a/tests/seqtk_seq_wrong_name.cwl b/tests/seqtk_seq_wrong_name.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 id: "seqtk_seq"
diff --git a/tests/test_bad_outputs_wf.cwl b/tests/test_bad_outputs_wf.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: Workflow
 inputs: []
diff --git a/tests/wf/badout1.cwl b/tests/wf/badout1.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 baseCommand: touch
diff --git a/tests/wf/badout2.cwl b/tests/wf/badout2.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 baseCommand: touch
diff --git a/tests/wf/badout3.cwl b/tests/wf/badout3.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 baseCommand: touch
diff --git a/tests/wf/cat.cwl b/tests/wf/cat.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 inputs:
diff --git a/tests/wf/count-lines1-wf.cwl b/tests/wf/count-lines1-wf.cwl
diff --git a/tests/wf/default_path.cwl b/tests/wf/default_path.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 inputs:
diff --git a/tests/wf/echo.cwl b/tests/wf/echo.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 inputs:
diff --git a/tests/wf/expect_packed.cwl b/tests/wf/expect_packed.cwl
@@ -127,4 +127,4 @@
             "id": "#sorttool.cwl"
         }
     ]
-}
+}
diff --git a/tests/wf/formattest.cwl b/tests/wf/formattest.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 $namespaces:
   edam: "http://edamontology.org/"
 cwlVersion: v1.0
diff --git a/tests/wf/hello-workflow.cwl b/tests/wf/hello-workflow.cwl
diff --git a/tests/wf/hello_single_tool.cwl b/tests/wf/hello_single_tool.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: echo
diff --git a/tests/wf/js_output.cwl b/tests/wf/js_output.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 requirements:
diff --git a/tests/wf/js_output_workflow.cwl b/tests/wf/js_output_workflow.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: Workflow
 cwlVersion: v1.0
 requirements:
diff --git a/tests/wf/listing_deep.cwl b/tests/wf/listing_deep.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 $namespaces:
diff --git a/tests/wf/listing_none.cwl b/tests/wf/listing_none.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 $namespaces:
diff --git a/tests/wf/listing_shallow.cwl b/tests/wf/listing_shallow.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 $namespaces:
diff --git a/tests/wf/listing_v1_0.cwl b/tests/wf/listing_v1_0.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 inputs:
diff --git a/tests/wf/missing_cwlVersion.cwl b/tests/wf/missing_cwlVersion.cwl
diff --git a/tests/wf/mut.cwl b/tests/wf/mut.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: Workflow
 inputs:
diff --git a/tests/wf/mut2.cwl b/tests/wf/mut2.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: Workflow
 inputs:
diff --git a/tests/wf/mut3.cwl b/tests/wf/mut3.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: Workflow
 inputs:
diff --git a/tests/wf/parseInt-tool.cwl b/tests/wf/parseInt-tool.cwl
diff --git a/tests/wf/revsort.cwl b/tests/wf/revsort.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 #
 # This is a two-step workflow which uses "revtool" and "sorttool" defined above.
 #
diff --git a/tests/wf/revtool.cwl b/tests/wf/revtool.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 #
 # Simplest example command line program wrapper for the Unix tool "rev".
 #
diff --git a/tests/wf/scatterfail.cwl b/tests/wf/scatterfail.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: Workflow
 cwlVersion: v1.0
 requirements:
diff --git a/tests/wf/sorttool.cwl b/tests/wf/sorttool.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 # Example command line program wrapper for the Unix tool "sort"
 # demonstrating command line flags.
 class: CommandLineTool
diff --git a/tests/wf/updatedir.cwl b/tests/wf/updatedir.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 requirements:
diff --git a/tests/wf/updatedir_inplace.cwl b/tests/wf/updatedir_inplace.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 $namespaces:
diff --git a/tests/wf/updateval.cwl b/tests/wf/updateval.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 requirements:
diff --git a/tests/wf/updateval_inplace.cwl b/tests/wf/updateval_inplace.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 $namespaces:
diff --git a/tests/wf/wc-tool.cwl b/tests/wf/wc-tool.cwl
diff --git a/tests/wf/wffail.cwl b/tests/wf/wffail.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: Workflow
 cwlVersion: v1.0
 inputs: []
diff --git a/tests/wf/wrong_cwlVersion.cwl b/tests/wf/wrong_cwlVersion.cwl

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,4 @@`
	`1`	`+#!/usr/bin/env cwl-runner`
`1`	`2`	`class: Workflow`
`2`	`3`	`cwlVersion: v1.0`
`3`	`4`	`requirements:`