add vv raw reads stub

Author: torres-alexis

RNAseq/Workflow_Documentation/NF_RCP/workflow_code/bin/vv.py

@@ -0,0 +1,137 @@
+#!/usr/bin/env python
+import click
+from pathlib import Path
+import json
+import os
+
+# Output structure config
+STRUCTURE = {
+    "rnaseq": {
+        "microbes": {
+            "components": {
+                "raw_reads": {
+                    "outputs": {
+                        "raw_fastq": "00-RawData/Fastq",
+                        "raw_fastqc": "00-RawData/FastQC_Reports",
+                        "raw_multiqc": "00-RawData/FastQC_Reports"
+                    }
+                },
+                "trimmed_reads": {
+                    "outputs": {
+                        "fastq": "01-TG_Preproc/Fastq",
+                        "fastqc": "01-TG_Preproc/FastQC_Reports",
+                        "trimming_reports": "01-TG_Preproc/Trimming_Reports"
+                    }
+                },
+                "alignments": {
+                    "02-Bowtie2_Alignment": {
+                        "{sample_name}": {}  # Sample-specific subdirectories
+                    }
+                },
+                "counts": {
+                    "03-FeatureCounts": {
+                    }
+                },
+                "dge": {
+                    "04-DESeq2_NormCounts": {},
+                    "04-rRNArm_DESeq2_NormCounts": {},
+                    "05-rRNArm_DESeq2_DGE": {},
+                    "05-DESeq2_DGE": {}
+                }
+            }
+        }
+    }
+}
+
+# Future tissue-specific structure could look like:
+TISSUE_STRUCTURE = {
+    "dge": {
+        "04-{tissue}-DESeq2_NormCounts": {},
+        "04-{tissue}-rRNArm_DESeq2_NormCounts": {},
+        "05-{tissue}-rRNArm_DESeq2_DGE": {},
+        "05-{tissue}-DESeq2_DGE": {}
+    }
+}
+
+@click.command()
+@click.option('--assay-type', type=click.Choice(['rnaseq', 'scrna']), default='rnaseq')
+@click.option('--assay-suffix', type=click.STRING, default="_GLbulkRNAseq")
+@click.option('--runsheet-path', type=click.Path(exists=True), help="Path to runsheet")
+@click.option('--outdir', type=click.Path(), default=Path.cwd(), help="Output directory")
+@click.option('--paired-end', type=click.STRING, help="Paired end setting")
+@click.option('--mode', type=click.Choice(['microbes', 'default']), default='default')
+@click.option('--run-components', type=click.STRING, help="Component to validate (e.g. raw_reads)")
+@click.option('--raw-fastq', type=click.Path(exists=True), help="Path to raw fastq directory")
+@click.option('--raw-fastqc', type=click.Path(exists=True), help="Path to raw fastqc directory")
+@click.option('--raw-multiqc', type=click.Path(exists=True), help="Path to raw multiqc directory")
+def vv(assay_type, assay_suffix, runsheet_path, outdir, paired_end, mode, run_components, raw_fastq, raw_fastqc, raw_multiqc):
+    """Organize pipeline outputs and optionally validate"""
+    outdir = Path(outdir)
+    
+    # Stage files if inputs provided
+    if any([raw_fastq, raw_fastqc, raw_multiqc]):
+        file_paths = {
+            'raw_fastq': raw_fastq,
+            'raw_fastqc': raw_fastqc,
+            'raw_multiqc': raw_multiqc
+        }
+        stage_files(assay_type, 'raw_reads', **file_paths)
+    
+    # Run validation if component specified
+    if run_components:
+        with open("VV_log.tsv", "w") as f:
+            f.write(f"Stub validation log for {run_components}\n")
+
+def stage_files(assay_type, section, **file_paths):
+    """
+    Stage files either by component or direct paths
+    
+    Args:
+        assay_type (str): e.g. 'rnaseq'
+        section (str): e.g. 'raw_reads'
+        **file_paths: Keyword args for direct file paths (raw_fastq, raw_fastqc, etc)
+    """
+    structure = STRUCTURE[assay_type]['microbes']['components'][section]['outputs']
+    
+    # Direct path staging
+    for file_type, path in file_paths.items():
+        if path:  # Only process if path was provided
+            target_dir = structure[file_type]
+            stage_to_location(path, target_dir)
+
+def stage_to_location(source_path, target_dir):
+    """Helper to stage files to their target location"""
+    os.makedirs(target_dir, exist_ok=True)
+    
+    # Get the ultimate source by following all symlinks
+    ultimate_source = os.path.realpath(source_path)
+    
+    if os.path.isdir(source_path):
+        # For directories, link their contents directly into target_dir
+        for item in os.listdir(source_path):
+            src = os.path.realpath(os.path.join(source_path, item))  # Get ultimate source for each file
+            dst = os.path.join(target_dir, item)
+            os.symlink(src, dst)
+    else:
+        # For single files
+        dst = os.path.join(target_dir, os.path.basename(source_path))
+        os.symlink(ultimate_source, dst)
+
+def get_target_dir(structure, file_type):
+    """Traverse structure to find target directory for file type"""
+    # Implementation depends on your exact structure format
+    pass
+
+if __name__ == '__main__':
+    vv()
+
+# Component based:
+stage_files('rnaseq', 'raw_reads', 
+           components=['raw_reads'],
+           raw_fastq='path/to/fastq',
+           raw_fastqc='path/to/fastqc')
+
+# Direct path based:
+stage_files('rnaseq', 'raw_reads',
+           raw_fastq='path/to/fastq',
+           raw_fastqc='path/to/fastqc')