Fix generate report

Author: aditigopalan

.DS_Store

@@ -0,0 +1,3 @@
+repo_url
+https://github.com/PythonOT/POT.git
+https://github.com/RabadanLab/TARGet.git

.nextflow/.DS_Store

@@ -4,18 +4,21 @@ nextflow.enable.dsl=2
 /**
  * Process: GenerateReport
  * 
- * Generates a consolidated report from all status files.
- * The report includes:
- * - Repository name
- * - Clone status
- * - Dependencies status
- * - Tests status
- * - Almanack status
+ * Aggregates all status files into a single consolidated CSV report.
+ * The report includes the following columns:
+ * - Tool: Repository name
+ * - CloneRepository: Status of repository cloning
+ * - CheckReadme: Status of README check
+ * - CheckDependencies: Status of dependencies check
+ * - CheckTests: Status of tests check
+ * - Almanack: Status of Almanack analysis
  */
 
 process GenerateReport {
+    publishDir path: "${params.output_dir}", mode: 'copy'
+    
     input:
-        path "*status_*.txt"
+        path status_files
 
     output:
         path "consolidated_report.csv"
@@ -25,12 +28,16 @@ process GenerateReport {
     #!/bin/bash
     set -euo pipefail
 
-    # Create header
-    echo "repo_name,clone_status,deps_status,tests_status,almanack_status" > consolidated_report.csv
-
-    # Append each status file
-    for f in status_*.txt; do
-        cat "\$f" >> consolidated_report.csv
+    # Write header with column names
+    echo "Tool,CloneRepository,CheckReadme,CheckDependencies,CheckTests,Almanack" > consolidated_report.csv
+    
+    # Append each status row from all files
+    for f in ${status_files}; do
+        if [ -f "\$f" ]; then
+            cat "\$f" >> consolidated_report.csv
+        else
+            echo "Warning: File \$f not found" >&2
+        fi
     done
     """
 }

example-input.csv

@@ -0,0 +1,3 @@
+Tool,CloneRepository,CheckReadme,CheckDependencies,CheckTests,Almanack
+TARGet,PASS,FAIL,FAIL,PASS
+POT,PASS,PASS,PASS,PASS