From fcc593adf187a1294c657e79bb3ec2ed49ea4d78 Mon Sep 17 00:00:00 2001
From: Peter Amstutz <peter.amstutz@curoverse.com>
Date: Mon, 27 Mar 2017 10:32:36 -0400
Subject: [PATCH] Fix identifier conflicts (checked by cwltool for the first
 time) by giving ids to embedded tools and workflows.

---
 v1.0/v1.0/count-lines10-wf.cwl                    | 1 +
 v1.0/v1.0/count-lines2-wf.cwl                     | 1 +
 v1.0/v1.0/scatter-valuefrom-wf1.cwl               | 1 +
 v1.0/v1.0/scatter-valuefrom-wf5.cwl               | 1 +
 v1.0/v1.0/scatter-wf1.cwl                         | 1 +
 v1.1.0-dev1/v1.1.0-dev1/count-lines10-wf.cwl      | 1 +
 v1.1.0-dev1/v1.1.0-dev1/count-lines2-wf.cwl       | 1 +
 v1.1.0-dev1/v1.1.0-dev1/scatter-valuefrom-wf1.cwl | 1 +
 v1.1.0-dev1/v1.1.0-dev1/scatter-valuefrom-wf5.cwl | 1 +
 v1.1.0-dev1/v1.1.0-dev1/scatter-wf1.cwl           | 1 +
 10 files changed, 10 insertions(+)

diff --git a/v1.0/v1.0/count-lines10-wf.cwl b/v1.0/v1.0/count-lines10-wf.cwl
index 63d9f0ff1..cb55a7705 100755
--- a/v1.0/v1.0/count-lines10-wf.cwl
+++ b/v1.0/v1.0/count-lines10-wf.cwl
@@ -13,6 +13,7 @@ steps:
     out: [count_output]
     run:
       class: Workflow
+      id: subwf
       inputs:
         file1: File
       outputs:
diff --git a/v1.0/v1.0/count-lines2-wf.cwl b/v1.0/v1.0/count-lines2-wf.cwl
index be564beaf..171de950d 100755
--- a/v1.0/v1.0/count-lines2-wf.cwl
+++ b/v1.0/v1.0/count-lines2-wf.cwl
@@ -39,6 +39,7 @@ steps:
     out: [parseInt_output]
     run:
       class: ExpressionTool
+      id: subtool
       inputs:
         parseInt_file1:
           type: File
diff --git a/v1.0/v1.0/scatter-valuefrom-wf1.cwl b/v1.0/v1.0/scatter-valuefrom-wf1.cwl
index f38d1ed15..78ba28ed7 100644
--- a/v1.0/v1.0/scatter-valuefrom-wf1.cwl
+++ b/v1.0/v1.0/scatter-valuefrom-wf1.cwl
@@ -35,6 +35,7 @@ steps:
     scatter: echo_in
     run:
       class: CommandLineTool
+      id: subtool
       inputs:
         first:
           type: string
diff --git a/v1.0/v1.0/scatter-valuefrom-wf5.cwl b/v1.0/v1.0/scatter-valuefrom-wf5.cwl
index 016eebfd4..3ac1f24dd 100644
--- a/v1.0/v1.0/scatter-valuefrom-wf5.cwl
+++ b/v1.0/v1.0/scatter-valuefrom-wf5.cwl
@@ -35,6 +35,7 @@ steps:
     scatter: echo_in
     run:
       class: CommandLineTool
+      id: subtool
       inputs:
         first:
           type: string
diff --git a/v1.0/v1.0/scatter-wf1.cwl b/v1.0/v1.0/scatter-wf1.cwl
index d47065860..7e7f52bc8 100644
--- a/v1.0/v1.0/scatter-wf1.cwl
+++ b/v1.0/v1.0/scatter-wf1.cwl
@@ -19,6 +19,7 @@ steps:
     scatter: echo_in
     run:
       class: CommandLineTool
+      id: subtool
       inputs:
         echo_in:
           type: string
diff --git a/v1.1.0-dev1/v1.1.0-dev1/count-lines10-wf.cwl b/v1.1.0-dev1/v1.1.0-dev1/count-lines10-wf.cwl
index 5714cd913..c0c34348a 100755
--- a/v1.1.0-dev1/v1.1.0-dev1/count-lines10-wf.cwl
+++ b/v1.1.0-dev1/v1.1.0-dev1/count-lines10-wf.cwl
@@ -13,6 +13,7 @@ steps:
     out: [count_output]
     run:
       class: Workflow
+      id: subwf
       inputs:
         file1: File
       outputs:
diff --git a/v1.1.0-dev1/v1.1.0-dev1/count-lines2-wf.cwl b/v1.1.0-dev1/v1.1.0-dev1/count-lines2-wf.cwl
index d0bb8d4ac..ceaeef6c6 100755
--- a/v1.1.0-dev1/v1.1.0-dev1/count-lines2-wf.cwl
+++ b/v1.1.0-dev1/v1.1.0-dev1/count-lines2-wf.cwl
@@ -39,6 +39,7 @@ steps:
     out: [parseInt_output]
     run:
       class: ExpressionTool
+      id: subtool
       inputs:
         parseInt_file1:
           type: File
diff --git a/v1.1.0-dev1/v1.1.0-dev1/scatter-valuefrom-wf1.cwl b/v1.1.0-dev1/v1.1.0-dev1/scatter-valuefrom-wf1.cwl
index b396700ef..cff199749 100644
--- a/v1.1.0-dev1/v1.1.0-dev1/scatter-valuefrom-wf1.cwl
+++ b/v1.1.0-dev1/v1.1.0-dev1/scatter-valuefrom-wf1.cwl
@@ -35,6 +35,7 @@ steps:
     scatter: echo_in
     run:
       class: CommandLineTool
+      id: subtool
       inputs:
         first:
           type: string
diff --git a/v1.1.0-dev1/v1.1.0-dev1/scatter-valuefrom-wf5.cwl b/v1.1.0-dev1/v1.1.0-dev1/scatter-valuefrom-wf5.cwl
index 3688f33f8..ad8f60b97 100644
--- a/v1.1.0-dev1/v1.1.0-dev1/scatter-valuefrom-wf5.cwl
+++ b/v1.1.0-dev1/v1.1.0-dev1/scatter-valuefrom-wf5.cwl
@@ -35,6 +35,7 @@ steps:
     scatter: echo_in
     run:
       class: CommandLineTool
+      id: subtool
       inputs:
         first:
           type: string
diff --git a/v1.1.0-dev1/v1.1.0-dev1/scatter-wf1.cwl b/v1.1.0-dev1/v1.1.0-dev1/scatter-wf1.cwl
index 1e5d62025..af7f950be 100644
--- a/v1.1.0-dev1/v1.1.0-dev1/scatter-wf1.cwl
+++ b/v1.1.0-dev1/v1.1.0-dev1/scatter-wf1.cwl
@@ -19,6 +19,7 @@ steps:
     scatter: echo_in
     run:
       class: CommandLineTool
+      id: subtool
       inputs:
         echo_in:
           type: string