line endings

.github/workflows/test-in-miniwdl.yml

@@ -1,27 +1,27 @@
-name: Miniwdl Test CI
-
-on:
-  push:
-    branches: [ "main" ]
-  pull_request:
-    branches: [ "main" ]
-
-jobs:
-
-  build:
-
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v4
-    - name: Install the dependencies
-      run: pip install -r requirements.txt
-
-    - name: Test Miniwdl
-      run: miniwdl run_self_test
-
-    - name: Check workflows
-      run: make check
-
-    - name: Run tests
-      run: make test
+name: Miniwdl Test CI
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Install the dependencies
+      run: pip install -r requirements.txt
+
+    - name: Test Miniwdl
+      run: miniwdl run_self_test
+
+    - name: Check workflows
+      run: make check
+
+    - name: Run tests
+      run: make test

.pytest_wdl_config.yml

@@ -1,11 +1,11 @@
-show_progress: true
-# proxies:
-#   http: 
-#     env: HTTP
-#     value: http://proxy.example.com:8080
-#   https: 
-#     env: HTTPS
-#     value: https://proxy.example.com:8080
-default_executors: 
-  - miniwdl
+show_progress: true
+# proxies:
+#   http: 
+#     env: HTTP
+#     value: http://proxy.example.com:8080
+#   https: 
+#     env: HTTPS
+#     value: https://proxy.example.com:8080
+default_executors: 
+  - miniwdl
   # - cromwell

assemblies.wdl

@@ -1,41 +1,49 @@
-# This project constitutes a work of the United States Government and is not
-# subject to domestic copyright protection under 17 USC § 105. No Rights Are 
-# Reserved.
-
-# This program is distributed in the hope that it will be useful. Responsibility
-# for the use of the system and interpretation of documentation and results lies
-# solely with the user. In no event shall FDA be liable for direct, indirect,
-# special, incidental, or consequential damages resulting from the use, misuse,
-# or inability to use the system and accompanying documentation. Third parties'
-# use of or acknowledgment of the system does not in any way represent that
-# FDA endorses such third parties or expresses any opinion with respect to their
-# statements. 
-
-# This program is free software: you can redistribute it and/or modify it.
-
-version 1.1
-
-task calculateN50 {
-
-    input {
-        File assembly
-    }
-
-    command <<<
-        seqtk comp ~{assembly} | cut -f 2 | sort -rn | awk '{ sum += $0; print $0, sum }' | tac | awk 'NR==1 { halftot=$2/2 } lastsize>halftot && $2<halftot { print $1 } { lastsize=$2 }'
-    >>>
-
-    output {
-        Int n50 = read_int(stdout())
-    }
-
-    runtime {
-        container: "staphb/seqtk:latest"
-        cpu: 1
-        memory: "512 MB"
-    }
-
-    parameter_meta {
-        assembly: "Assembly in FASTA format."
-    }
+# This project constitutes a work of the United States Government and is not
+# subject to domestic copyright protection under 17 USC § 105. No Rights Are 
+# Reserved.
+
+# This program is distributed in the hope that it will be useful. Responsibility
+# for the use of the system and interpretation of documentation and results lies
+# solely with the user. In no event shall FDA be liable for direct, indirect,
+# special, incidental, or consequential damages resulting from the use, misuse,
+# or inability to use the system and accompanying documentation. Third parties'
+# use of or acknowledgment of the system does not in any way represent that
+# FDA endorses such third parties or expresses any opinion with respect to their
+# statements. 
+
+# This program is free software: you can redistribute it and/or modify it.
+
+version 1.1
+
+import "identify.wdl"
+
+struct AssemblyInfo {
+    Int? n50
+    Float? coverage
+    Tool tool
+}
+
+task calculateN50 {
+
+    input {
+        File assembly
+    }
+
+    command <<<
+        seqtk comp ~{assembly} | cut -f 2 | sort -rn | awk '{ sum += $0; print $0, sum }' | tac | awk 'NR==1 { halftot=$2/2 } lastsize>halftot && $2<halftot { print $1 } { lastsize=$2 }'
+    >>>
+
+    output {
+        Int n50 = read_int(stdout())
+    }
+
+    runtime {
+        container: "staphb/seqtk:latest"
+        cpu: 1
+        memory: "512 MB"
+    }
+
+    parameter_meta {
+        assembly: "Assembly in FASTA format."
+    }
 }