Merge pull request #1 from tom-seqera/tiff-library

Add tiff library dependency
nf-core · Oct 30, 2024 · e3528f6 · e3528f6
2 parents 1958cfc + 726b50c
commit e3528f6
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Showing 6 changed files with 98 additions and 40 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,9 @@
 # Compiled class file
 *.class
 
+# intellij files
+.idea/
+
 # Log file
 *.log
 
@@ -26,4 +29,4 @@ hs_err_pid*
 /.project
 /.settings/
 /.nextflow/
-/.nf-test/
+/.nf-test/
diff --git a/dependency-reduced-pom.xml b/dependency-reduced-pom.xml
@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>com.nf-core</groupId>
+  <artifactId>nft-tiff</artifactId>
+  <name>nft-tiff</name>
+  <version>0.1.0</version>
+  <description>An nf-test plugin to test nft-tiff files</description>
+  <url>https://github.com/nf-core/nft-tiff</url>
+  <licenses>
+    <license>
+      <name>MIT License</name>
+      <url>http://www.opensource.org/licenses/mit</url>
+    </license>
+  </licenses>
+  <scm>
+    <connection>scm:git:https://github.com/nf-core/nft-tiff</connection>
+    <developerConnection>scm:git:ssh://github.com:nf-core/nft-tiff.git</developerConnection>
+    <url>https://github.com/nf-core/nft-tiff/tree/master</url>
+  </scm>
+  <build>
+    <plugins>
+      <plugin>
+        <artifactId>maven-shade-plugin</artifactId>
+        <version>3.5.2</version>
+        <executions>
+          <execution>
+            <phase>package</phase>
+            <goals>
+              <goal>shade</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+  </build>
+  <properties>
+    <maven.compiler.release>${java.version}</maven.compiler.release>
+    <java.version>11</java.version>
+    <maven.compiler.source>${java.version}</maven.compiler.source>
+    <maven.compiler.target>${java.version}</maven.compiler.target>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <additionalparam>-Xdoclint:none</additionalparam>
+  </properties>
+</project>
diff --git a/pom.xml b/pom.xml
@@ -1,38 +1,46 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0"
-	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-
-	<groupId>com.nf-core</groupId>
-	<artifactId>nft-tiff</artifactId>
-	<version>0.1.0</version>
-	<packaging>jar</packaging>
-
-	<name>nft-tiff</name>
-	<description>An nf-test plugin to test nft-tiff files</description>
-	<url>https://github.com/nf-core/nft-tiff</url>
-
-	<licenses>
-		<license>
-			<name>MIT License</name>
-			<url>http://www.opensource.org/licenses/mit</url>
-		</license>
-	</licenses>
-
-	<scm>
-		<url>https://github.com/nf-core/nft-tiff/tree/master</url>
-		<connection>scm:git:https://github.com/nf-core/nft-tiff</connection>
-		<developerConnection>scm:git:ssh://github.com:nf-core/nft-tiff.git</developerConnection>
-	</scm>
-
-	<properties>
-		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-		<java.version>11</java.version>
-		<maven.compiler.release>${java.version}</maven.compiler.release>
-		<maven.compiler.source>${java.version}</maven.compiler.source>
-		<maven.compiler.target>${java.version}</maven.compiler.target>
-		<additionalparam>-Xdoclint:none</additionalparam>
-	</properties>
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+
+  <groupId>com.nf-core</groupId>
+  <artifactId>nft-tiff</artifactId>
+  <version>0.1.0</version>
+  <packaging>jar</packaging>
+
+  <name>nft-tiff</name>
+  <description>An nf-test plugin to test nft-tiff files</description>
+  <url>https://github.com/nf-core/nft-tiff</url>
+
+  <licenses>
+    <license>
+      <name>MIT License</name>
+      <url>http://www.opensource.org/licenses/mit</url>
+    </license>
+  </licenses>
+
+  <scm>
+    <url>https://github.com/nf-core/nft-tiff/tree/master</url>
+    <connection>scm:git:https://github.com/nf-core/nft-tiff</connection>
+    <developerConnection>scm:git:ssh://github.com:nf-core/nft-tiff.git</developerConnection>
+  </scm>
+
+  <properties>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <java.version>11</java.version>
+    <maven.compiler.release>${java.version}</maven.compiler.release>
+    <maven.compiler.source>${java.version}</maven.compiler.source>
+    <maven.compiler.target>${java.version}</maven.compiler.target>
+    <additionalparam>-Xdoclint:none</additionalparam>
+  </properties>
+
+  <dependencies>
+    <dependency>
+      <groupId>mil.nga</groupId>
+      <artifactId>tiff</artifactId>
+      <version>3.0.0</version>
+    </dependency>
+  </dependencies>
 
   <build>
     <plugins>

diff --git a/...in/java/nf-core/nf/test/tiff/Methods.java → ...in/java/nf_core/nf/test/tiff/Methods.java b/...in/java/nf-core/nf/test/tiff/Methods.java → ...in/java/nf_core/nf/test/tiff/Methods.java
@@ -1,15 +1,17 @@
-package nf-core.nf.test.tiff;
+package nf_core.nf.test.tiff;
+
+import mil.nga.tiff.TIFFImage;
 
 /*
  * Add your custom methods to nf-test
  * 
  * @author: nf-core
  */
-
 public class Methods {
 
     public static void hello() {
         System.out.println("Hello from nft-tiff");
+        TIFFImage img = new TIFFImage();
     }
 
 }
diff --git a/...a/nf-core/nf/test/tiff/PathExtension.java → ...a/nf_core/nf/test/tiff/PathExtension.java b/...a/nf-core/nf/test/tiff/PathExtension.java → ...a/nf_core/nf/test/tiff/PathExtension.java
@@ -1,4 +1,4 @@
-package nf-core.nf.test.tiff;
+package nf_core.nf.test.tiff;
 
 /*
  * Add your custom extensions to the path() method

diff --git a/src/main/resources/META-INF/nf-test-plugin b/src/main/resources/META-INF/nf-test-plugin
@@ -1,5 +1,5 @@
 moduleName=nft-tiff
 moduleVersion=0.1.0
 moduleAuthors=nf-core
-extensionMethods=nf-core.nf.test.tiff.Methods
-extensionClasses=nf-core.nf.test.tiff.PathExtension
+extensionMethods=nf_core.nf.test.tiff.Methods
+extensionClasses=nf_core.nf.test.tiff.PathExtension