add zip and unzip function

src/main/java/nf_core/nf/test/utils/ZipUtils.java

@@ -0,0 +1,85 @@
+package nf_core.nf.test.utils;
+
+import java.io.BufferedOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.nio.file.FileVisitResult;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.SimpleFileVisitor;
+import java.nio.file.attribute.BasicFileAttributes;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+import java.util.zip.ZipOutputStream;
+
+public class ZipUtils {
+
+  public static void unzip(String zipFilePath, String destDirectory) throws IOException {
+    File destDir = new File(destDirectory);
+    if (!destDir.exists()) {
+      destDir.mkdirs();
+    }
+
+    try (ZipInputStream zipIn = new ZipInputStream(new FileInputStream(zipFilePath))) {
+      ZipEntry entry = zipIn.getNextEntry();
+      while (entry != null) {
+        String filePath = destDirectory + File.separator + entry.getName();
+        if (!entry.isDirectory()) {
+          extractFile(zipIn, filePath);
+        } else {
+          File dir = new File(filePath);
+          dir.mkdirs();
+        }
+        zipIn.closeEntry();
+        entry = zipIn.getNextEntry();
+      }
+    }
+  }
+
+  private static void extractFile(ZipInputStream zipIn, String filePath) throws IOException {
+    File file = new File(filePath);
+
+    // Create parent directories if they don't exist
+    File parent = file.getParentFile();
+    if (parent != null && !parent.exists()) {
+      parent.mkdirs();
+    }
+
+    // If the entry is a directory, just create it and return
+    if (filePath.endsWith(File.separator)) {
+      file.mkdirs();
+      return;
+    }
+
+    // Extract the file
+    try (BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(file))) {
+      byte[] bytesIn = new byte[4096];
+      int read;
+      while ((read = zipIn.read(bytesIn)) != -1) {
+        bos.write(bytesIn, 0, read);
+      }
+    }
+  }
+
+  public static void zip(String sourceDirPath, String zipFilePath) throws IOException {
+    Path zipFile = Files.createFile(Paths.get(zipFilePath));
+    try (ZipOutputStream zipOut = new ZipOutputStream(Files.newOutputStream(zipFile))) {
+      Path sourceDir = Paths.get(sourceDirPath);
+      Files.walkFileTree(sourceDir, new SimpleFileVisitor<Path>() {
+        @Override
+        public FileVisitResult visitFile(Path file, BasicFileAttributes attributes) throws IOException {
+          Path targetFile = sourceDir.relativize(file);
+          zipOut.putNextEntry(new ZipEntry(targetFile.toString()));
+          byte[] bytes = Files.readAllBytes(file);
+          zipOut.write(bytes, 0, bytes.length);
+          zipOut.closeEntry();
+          return FileVisitResult.CONTINUE;
+        }
+      });
+    }
+  }
+
+}

src/main/java/nf_core/nf/test/utils/ZipUtilsWrapper.groovy

@@ -0,0 +1,11 @@
+package nf_core.nf.test.utils
+
+class ZipUtilsWrapper {
+    static void unzip(String zipFilePath, String destDirectory) {
+        ZipUtils.unzip(zipFilePath, destDirectory)
+    }
+
+    static void zip(String sourceDirPath, String zipFilePath) {
+        ZipUtils.zip(sourceDirPath, zipFilePath)
+    }
+}

tests/unzip/main.nf

@@ -0,0 +1,10 @@
+workflow {
+
+  ch_stable_content = Channel
+    .of(
+      """
+    I HAVE STABLE CONTENT
+    """.stripIndent().trim()
+    )
+    .collectFile(storeDir: "${params.outdir}/stable", name: 'stable_content.txt', sort: true, newLine: true)
+}

tests/unzip/main.nf.test

@@ -0,0 +1,26 @@
+import nf_core.nf.test.utils.ZipUtilsWrapper
+
+nextflow_pipeline {
+
+    name "Test unzip"
+    script "./main.nf"
+    tag "unzip"
+
+    test("unzip") {
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+          ZipUtilsWrapper.zip("${params.outdir}/stable/stable_content.txt", "${params.outdir}/stable_content.zip")
+          ZipUtilsWrapper.unzip("${params.outdir}/stable_content.zip", "${params.outdir}/stable_content_unzipped/")
+          def stable_name = getAllFilesFromDir(params.outdir, true, [''], null, ['**'])
+          assert snapshot(
+            stable_name
+          ).match()
+        }
+    }
+}
+

tests/unzip/main.nf.test.snap

@@ -0,0 +1,21 @@
+{
+    "unzip": {
+        "content": [
+            [
+                [
+                    "stable_content.txt:md5,f6d73f703cda1c725ea78369a6c3a48d"
+                ],
+                "stable_content.txt:md5,f6d73f703cda1c725ea78369a6c3a48d",
+                "stable_content.zip:md5,ba7d71d2c8e3cd2a47fa1b498da44e99",
+                [
+
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-16T17:57:07.994203269"
+    }
+}