Create 1.1.3FastqgzNamed_selectAll_notGlob.wdl

_SRAtoFastqgz/1.1.3FastqgzNamed_selectAll_notGlob.wdl

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+version 1.0
+
+task rename_fastq_files_based_on_size {
+  input {
+    Array[File] fastq_file_paths
+    String sample_name
+    String disk_space = "150 GB"
+    Int cpu = 1 
+  }
+
+  command <<<
+    python3 <<CODE
+    import os
+    import shutil
+
+    # Convert file paths from WDL array to Python list
+    files = ["~{sep='", "' fastq_file_paths}"]
+    sample_name = "~{sample_name}"
+
+    # Calculate file sizes and sort them
+    file_sizes = [(f, os.path.getsize(f)) for f in files]
+    file_sizes.sort(key=lambda x: x[1])
+
+    # Initialize variables to hold file paths
+    i1_file, r1_file, r2_file = None, None, None
+
+    # Determine the number of files and assign accordingly
+    if len(files) == 2:
+        r1_file, r2_file = file_sizes[0][0], file_sizes[1][0]
+    elif len(files) == 3:
+        i1_file, r1_file, r2_file = file_sizes[0][0], file_sizes[1][0], file_sizes[2][0]
+
+    # Define new filenames
+    i1_new_filename = f"{sample_name}_S1_L001_I1_001.fastq.gz" if i1_file else None
+    r1_new_filename = f"{sample_name}_S1_L001_R1_001.fastq.gz"
+    r2_new_filename = f"{sample_name}_S1_L001_R2_001.fastq.gz"
+
+    # Copy and rename files
+    if i1_file:
+        shutil.copy2(i1_file, i1_new_filename)
+    shutil.copy2(r1_file, r1_new_filename)
+    shutil.copy2(r2_file, r2_new_filename)
+
+    # Output new filenames for verification
+    if i1_new_filename:
+        print(i1_new_filename)
+    print(r1_new_filename)
+    print(r2_new_filename)
+    CODE
+    ls -l
+  >>>
+
+  output {
+    String sample_name_out = sample_name
+    File r1 = "${sample_name}_S1_L001_R1_001.fastq.gz"
+    File r2 = "${sample_name}_S1_L001_R2_001.fastq.gz"
+    File? i1 = "${sample_name}_S1_L001_I1_001.fastq.gz"
+    # 如果有时候没有I1数据，就在命令中不处理或生成空文件，让其存在但不影响结果
+    Array[File] renamed_fastq_files = select_all([i1, r1, r2])
+  }
+
+  runtime {
+    docker: "registry-vpc.miracle.ac.cn/gznl/ooaahhdocker/python_pigz:1.0"
+    cpu: cpu
+    disk: disk_space
+  }
+}
+