stdin.patch

stdin.patch

From c707f01ec5192ec4eef75e55e89764d2203c8640 Mon Sep 17 00:00:00 2001
From: Renato Alves <alves.rjc@gmail.com>
Date: Tue, 16 Jan 2018 11:45:39 +0100
Subject: [PATCH] TST Test enforcing of filetype with 'filetype:fq3'

---
 tests/externalModuleFiletype/Modules/test.ngm/0.0/command.sh  |  8 ++++++++
 tests/externalModuleFiletype/Modules/test.ngm/0.0/module.yaml | 10 ++++++++++
 tests/externalModuleFiletype/sample.fq                        |  1 +
 tests/externalModuleFiletype/test.ngl                         | 11 +++++++++++
 4 files changed, 30 insertions(+)
 create mode 100755 tests/externalModuleFiletype/Modules/test.ngm/0.0/command.sh
 create mode 100644 tests/externalModuleFiletype/Modules/test.ngm/0.0/module.yaml
 create mode 120000 tests/externalModuleFiletype/sample.fq
 create mode 100644 tests/externalModuleFiletype/test.ngl

diff --git a/tests/externalModuleFiletype/Modules/test.ngm/0.0/command.sh b/tests/externalModuleFiletype/Modules/test.ngm/0.0/command.sh
new file mode 100755
index 0000000..908ddb7
--- /dev/null
+++ b/tests/externalModuleFiletype/Modules/test.ngm/0.0/command.sh
@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+echo "$*"
+
+if [ "$#" -ne 3 ]; then
+    echo "Expected 3 arguments, saw $#"
+    exit 1
+fi
diff --git a/tests/externalModuleFiletype/Modules/test.ngm/0.0/module.yaml b/tests/externalModuleFiletype/Modules/test.ngm/0.0/module.yaml
new file mode 100644
index 0000000..e2afb6a
--- /dev/null
+++ b/tests/externalModuleFiletype/Modules/test.ngm/0.0/module.yaml
@@ -0,0 +1,10 @@
+version: '0.0.0'
+name: 'Test tool'
+functions:
+    -
+        nglName: "testing_fq3"
+        arg0: './command.sh'
+
+        arg1:
+            atype: 'readset'
+            filetype: 'fq3'
diff --git a/tests/externalModuleFiletype/sample.fq b/tests/externalModuleFiletype/sample.fq
new file mode 120000
index 0000000..8d45525
--- /dev/null
+++ b/tests/externalModuleFiletype/sample.fq
@@ -0,0 +1 @@
+../select/sample.fq
\ No newline at end of file
diff --git a/tests/externalModuleFiletype/test.ngl b/tests/externalModuleFiletype/test.ngl
new file mode 100644
index 0000000..6baa14a
--- /dev/null
+++ b/tests/externalModuleFiletype/test.ngl
@@ -0,0 +1,11 @@
+ngless '0.0'
+local import "test" version "0.0"
+
+input = fastq('sample.fq')
+testing_fq3(input)
+
+input = paired('sample.fq', 'sample.fq')
+testing_fq3(input)
+
+input = paired('sample.fq', 'sample.fq', singles='sample.fq')
+testing_fq3(input)
-- 
2.15.1