find a way to use relative path in input csv file. Change test file name to be different that the AliNe one and avoid confusion whoch file is really used

Author: Juke34

data/chr21/chr21_small_mix.csv

@@ -1,4 +1,4 @@
 sample,input_1,input_2,strandedness,read_type
-test1,data/chr21/chr21_small_R1.fastq.gz,data/chr21/chr21_small_R2.fastq.gz,auto,short_paired
-test2,data/chr21/chr21_small_single.fastq.gz,,ISR,short_single
-test3,data/chr21/chr21sample2_small.bam,,ISR,short_paired
+test1,data/chr21/rain_chr21_small_R1.fastq.gz,data/chr21/rain_chr21_small_R2.fastq.gz,auto,short_paired
+test2,data/chr21/rain_chr21_small_single.fastq.gz,,ISR,short_single
+test3,data/chr21/rain_chr21sample2_small.bam,,ISR,short_paired

data/chr21/chr21_small_paired.csv

@@ -1,2 +1,2 @@
 sample,input_1,input_2,strandedness,read_type
-test1,data/chr21/chr21_small_R1.fastq.gz,data/chr21/chr21_small_R2.fastq.gz,auto,short_single
+test1,data/chr21/rain_chr21_small_R1.fastq.gz,data/chr21/rain_chr21_small_R2.fastq.gz,auto,short_single

data/chr21/chr21_small_single.csv

@@ -1,3 +1,3 @@
 sample,input_1,input_2,strandedness,read_type
-test1,data/chr21/chr21_small_R1.fastq.gz,,auto,short_single
-test2,data/chr21/chr21_small_R2.fastq.gz,,ISR,short_single
+test1,data/chr21/rain_chr21_small_R1.fastq.gz,,auto,short_single
+test2,data/chr21/rain_chr21_small_R2.fastq.gz,,ISR,short_single

data/chr21/chr21_small_single.fastq.gz

@@ -0,0 +1 @@
+rain_chr21_small_R1.fastq.gz

data/chr21/chr21_small_R1.fastq.gz data/chr21/rain_chr21_small_R1.fastq.gzdata/chr21/chr21_small_R1.fastq.gz renamed to data/chr21/rain_chr21_small_R1.fastq.gz

@@ -80,4 +80,17 @@ class RainUtils {
                 .replaceAll(/\.bam$/, '')        // Remove .bam
         }
     } 
+    // Function to get absolute path from relative or absolute input
+    public static String getAbsolutePath( path ) {
+        if (!path) return null
+        def trimmedPath = path.toString().trim()
+        def f = new File(trimmedPath)
+        
+        // If path is already absolute, return it
+        if (f.isAbsolute()) {
+            return f.toString()
+        }
+        f = f.getAbsoluteFile()
+         return f.toString()
+    }
 }

data/chr21/chr21_small_R2.fastq.gz data/chr21/rain_chr21_small_R2.fastq.gzdata/chr21/chr21_small_R2.fastq.gz renamed to data/chr21/rain_chr21_small_R2.fastq.gz

@@ -124,9 +124,9 @@ process create_aline_csv_he {
  * Collect CSV files for AliNe input from converted FASTQ reads
  * Generates a single CSV with columns: sample,fastq_1,fastq_2,strandedness,read_type
  */
-process collect_aline_csv_he {
+process collect_aline_csv {
     label 'bash'
-    publishDir("${output_dir}", mode:"copy", pattern: "*.csv")
+    publishDir("${params.outdir}/${output_dir}", mode:"copy", pattern: "*.csv")
 
     input:
         val all_csv  // List of tuples (meta, fastq_files)
@@ -141,9 +141,36 @@ process collect_aline_csv_he {
         list_csv = all_csv
         list_csv_bash = list_csv.join(" "); // remove bracket and replace comma by space to be processed by bash
         """
-        echo "sample,fastq_1,fastq_2,strandedness,read_type" > hyper_editing_samples.csv
+        echo "sample,fastq_1,fastq_2,strandedness,read_type" > aline_input.csv
         for entry in ${list_csv_bash}; do
-            cat \$entry >> hyper_editing_samples.csv
+            cat \$entry >> aline_input.csv
         done
         """
+}
+
+/*
+ * Recreate CSV file with absolute paths from metadata
+ * Takes input samples with metadata and generates a new CSV with absolute file paths
+ * This allows conversion of relative paths to absolute paths for CI/CD compatibility
+ */
+process recreate_csv_with_abs_paths {
+    label 'bash'
+    tag "${meta.uid}"
+    
+    input:
+        tuple val(meta), path(file) 
+
+    output:
+        path "*.csv", emit: csv
+
+    script:
+        
+        def sample_id = meta.sample_id
+        def strandedness = meta.strandedness
+        def read_type = meta.read_type
+        def file1 = meta.file_abspath[0]
+        def file2 = meta.file_abspath[1] ? meta.file_abspath[1] : ""
+        """
+        echo "${sample_id},${file1},${file2},${strandedness},${read_type}" > ${meta.uid}.csv
+        """
 }