Merge pull request #16 from maxulysse/getRelativePath

Add getRelativePath() function

README.md

@@ -77,6 +77,72 @@ assert snapshot(
 
 First argument is the pipeline `outdir` directory path, second is a boolean to include folders, and the third is a list of glob patterns to ignore, and the fourth is a file containing a list of glob patterns to ignore.
 
+## `getRelativePath()`
+
+This function is used to get the relative path from a list of files compared to a given directory.
+
+```bash
+results/
+├── pipeline_info
+│   └── execution_trace_2024-09-30_13-10-16.txt
+└── stable
+    ├── stable_content.txt
+    └── stable_name.txt
+
+2 directories, 3 files
+```
+
+Following the previous example, we want to get the relative path of the stable paths in the `results` directory.
+
+```groovy
+def stable_name    = getAllFilesFromDir(params.outdir, true, ['pipeline_info/execution_*.{html,txt}'], null )
+```
+
+The `stable_name` variable contains the list of stable files and folders in the `results` directory.
+
+```groovy
+assert snapshot(
+  getRelativePath(stable_name, outputDir)
+).match()
+```
+
+By using `getRelativePath()` we generate in the snapshot:
+
+```text
+"content": [
+    [
+        "pipeline_info",
+        "stable",
+        "stable/stable_content.txt",
+        "stable/stable_name.txt"
+    ]
+]
+```
+
+A reduced list can be generated by using the `getAllFilesFromDir()` not to output the folders.
+
+```text
+"content": [
+    [
+        "stable/stable_content.txt",
+        "stable/stable_name.txt"
+    ]
+]
+```
+
+While only a flat structure would be generated without using `getRelativePath()` and using `*.name` to capture the file names.
+
+```text
+"content": [
+    [
+        "pipeline_info",
+        "stable",
+        "stable_content.txt",
+        "stable_name.txt"
+    ]
+]
+```
+
 ## Credits
 
 nft-utils was created by the nf-core community.

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

@@ -110,4 +110,15 @@ private static List<String> readGlobsFromFile(String filePath) throws IOExceptio
     }
     return globs;
   }
+
+  public static List<String> getRelativePath(List<File> filePaths, String baseDir) {
+    Path basePath = Paths.get(baseDir).toAbsolutePath().normalize();
+
+    return filePaths.stream()
+        .map(filePath -> {
+          Path path = Paths.get(filePath.toURI()).toAbsolutePath().normalize();
+          return basePath.relativize(path).toString();
+        })
+        .collect(Collectors.toList());
+  }
 }

tests/getRelativePath/main.nf

@@ -0,0 +1,23 @@
+workflow {
+
+    def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+
+    ch_stable_content = Channel.of(
+    """
+    I HAVE STABLE CONTENT
+    """.stripIndent().trim())
+    .collectFile(storeDir: "${params.outdir}/stable", name: 'stable_content.txt', sort: true, newLine: true)
+
+    ch_stable_name = Channel.of(
+    """
+    I DO NOT HAVE STABLE CONTENT
+    ${trace_timestamp}
+    """.stripIndent().trim())
+    .collectFile(storeDir: "${params.outdir}/stable", name: 'stable_name.txt', sort: true, newLine: true)
+
+    ch_unstable_name = Channel.of(
+    """
+    I DO NOT HAVE STABLE NAME
+    """.stripIndent().trim())
+    .collectFile(storeDir: "${params.outdir}/pipeline_info", name: "execution_trace_${trace_timestamp}.txt", sort: true, newLine: true)
+}

tests/getRelativePath/main.nf.test

@@ -0,0 +1,25 @@
+nextflow_pipeline {
+
+    name "Test getRelativePath"
+    script "./main.nf"
+    tag "getRelativePath"
+
+    test("getRelativePath") {
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+          // Use getAllFilesFromDir() to get a list of all files and folders from the output directory, minus the timestamped files
+          def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/execution_*.{html,txt}'], null )
+          def stable_file = getAllFilesFromDir(params.outdir, false, ['pipeline_info/execution_*.{html,txt}'], null )
+          assert snapshot(
+            // Use getRelativePath to get the relative path starting from outputDir
+            getRelativePath(stable_name, outputDir),
+            getRelativePath(stable_file, outputDir)
+          ).match()
+        }
+    }
+}

tests/getRelativePath/main.nf.test.snap

@@ -0,0 +1,21 @@
+{
+    "getRelativePath": {
+        "content": [
+            [
+                "pipeline_info",
+                "stable",
+                "stable/stable_content.txt",
+                "stable/stable_name.txt"
+            ],
+            [
+                "stable/stable_content.txt",
+                "stable/stable_name.txt"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-01T18:20:38.379963"
+    }
+}