stdin.patch

stdin.patch

From 6f52834bab888b6af9669f6dc97fb62accacb6b4 Mon Sep 17 00:00:00 2001
From: Renato Alves <alves.rjc@gmail.com>
Date: Tue, 16 Jan 2018 16:43:53 +0100
Subject: [PATCH] TST --search-dir should be expanded before passing to
 external module

---
 tests/searchdirExternalModule/Modules/test.ngm/0.0/command.sh  | 6 ++++++
 tests/searchdirExternalModule/Modules/test.ngm/0.0/module.yaml | 9 +++++++++
 tests/searchdirExternalModule/cmdargs                          | 1 +
 tests/searchdirExternalModule/sample.fq                        | 1 +
 tests/searchdirExternalModule/test.ngl                         | 4 ++++
 5 files changed, 21 insertions(+)
 create mode 100755 tests/searchdirExternalModule/Modules/test.ngm/0.0/command.sh
 create mode 100644 tests/searchdirExternalModule/Modules/test.ngm/0.0/module.yaml
 create mode 100644 tests/searchdirExternalModule/cmdargs
 create mode 120000 tests/searchdirExternalModule/sample.fq
 create mode 100644 tests/searchdirExternalModule/test.ngl

diff --git a/tests/searchdirExternalModule/Modules/test.ngm/0.0/command.sh b/tests/searchdirExternalModule/Modules/test.ngm/0.0/command.sh
new file mode 100755
index 0000000..a72529a
--- /dev/null
+++ b/tests/searchdirExternalModule/Modules/test.ngm/0.0/command.sh
@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+
+if [ "$1" != "/somedir/input.fq" ]; then
+    echo "Expected '/somedir/input.fq' saw '$1'"
+    exit 1
+fi
diff --git a/tests/searchdirExternalModule/Modules/test.ngm/0.0/module.yaml b/tests/searchdirExternalModule/Modules/test.ngm/0.0/module.yaml
new file mode 100644
index 0000000..cac4cd3
--- /dev/null
+++ b/tests/searchdirExternalModule/Modules/test.ngm/0.0/module.yaml
@@ -0,0 +1,9 @@
+version: '0.0.0'
+name: 'Test tool'
+functions:
+    -
+        nglName: "testing_searchdir"
+        arg0: './command.sh'
+
+        arg1:
+            atype: 'str'
diff --git a/tests/searchdirExternalModule/cmdargs b/tests/searchdirExternalModule/cmdargs
new file mode 100644
index 0000000..0326dfc
--- /dev/null
+++ b/tests/searchdirExternalModule/cmdargs
@@ -0,0 +1 @@
+--search-dir data=/somedir
diff --git a/tests/searchdirExternalModule/sample.fq b/tests/searchdirExternalModule/sample.fq
new file mode 120000
index 0000000..8d45525
--- /dev/null
+++ b/tests/searchdirExternalModule/sample.fq
@@ -0,0 +1 @@
+../select/sample.fq
\ No newline at end of file
diff --git a/tests/searchdirExternalModule/test.ngl b/tests/searchdirExternalModule/test.ngl
new file mode 100644
index 0000000..21c3ab8
--- /dev/null
+++ b/tests/searchdirExternalModule/test.ngl
@@ -0,0 +1,4 @@
+ngless '0.0'
+local import "test" version "0.0"
+
+testing_searchdir("<data>/input.fq")
-- 
2.15.1