Merge pull request #114 from jun-wan/master

Add new script for create rnaseq samplesheet

Author: aanil

create_rnaseq_samplesheet.py

@@ -0,0 +1,69 @@
+#!/usr/bin/env python3
+import os
+import sys
+import glob
+import argparse
+
+class CustomParser(argparse.ArgumentParser):
+    def print_help(self, file=None):
+        help_text = """
+
+Description:
+Generate an RNA-seq sample sheet for a given project before running the nf-core/rnaseq analysis pipeline.
+The resulting CSV is printed to the screen (stdout). To save the CSV to a file, use shell redirection.
+
+USAGE:
+  create_rnaseq_samplesheet.py <ProjectID> <Strandedness> [-d <data_path>] > <output.csv>
+
+Examples:
+  create_rnaseq_samplesheet.py P001 auto > P001.csv
+  create_rnaseq_samplesheet.py P001 auto -d /my/data/path > P001.csv
+
+Arguments:
+  ProjectID      Identifier for your RNA-seq project (e.g., P001)
+  Strandedness   Library strandedness (forward/reverse/unstranded/auto, use 'auto' to auto-detect)
+
+Optional arguments:
+  -d, --data     Path to your RNA-seq data folder. Default: /proj/ngi2016003/nobackup/NGI/DATA
+  -h, --help     Show this help message and exit
+"""
+        print(help_text)
+
+def main():
+    parser = CustomParser(add_help=False)
+    parser.add_argument("ProjectID", help="Identifier for your RNA-seq project (e.g., P001)")
+    parser.add_argument("Strandedness", help="Library strandedness (use 'auto' to auto-detect)")
+    parser.add_argument("-d", "--data", default="/proj/ngi2016003/nobackup/NGI/DATA",
+                        help="Path to RNA-seq data (default: %(default)s)")
+    parser.add_argument("-h", "--help", action="help", help="Show this help message and exit")
+
+    args = parser.parse_args()
+
+    # Generate CSV content
+    print(f"# Sample sheet for project {args.ProjectID}")
+    print(f"Strandedness,{args.Strandedness}")
+
+    # Build full path to project data
+    data_path = os.path.join(args.data, args.ProjectID)
+
+    if not os.path.exists(data_path):
+        sys.exit(f"Error: data path does not exist: {data_path}")
+
+    header = "sample,fastq_1,fastq_2,strandedness"
+    print(header)
+
+    sampleList = os.listdir(data_path)
+    sampleList.sort()
+
+    for sample in sampleList:
+        path_pattern = os.path.join(data_path, sample, '**', '*R1*.gz')
+        paths = glob.glob(path_pattern, recursive=True)
+
+        for counter, R1 in enumerate(paths, 1):
+            R2 = R1.replace('_R1_','_R2_')
+            print(f"{sample},{R1},{R2},{args.Strandedness}")
+
+
+if __name__ == "__main__":
+    main()
+