Move lablog_bam2fq.sh to RAW/ & Fix Path Issues

[OPSergio]

Summary

This PR moves lablog_bam2fq.sh to RAW/, corrects path and regex errors, and ensures that the BAM-to-FASTQ pipeline functions correctly.
Additionally, it adapts the _01_bam2fq.sh and _02_pgzip.sh scripts and introduces a new _03_symlink.sh to create symbolic links in ANALYSIS/00-reads/.

Main Changes & Fixes

1. Moved lablog_bam2fq.sh to RAW/

• Ensures all BAM-to-FASTQ processing happens inside RAW/.
• Prevents issues caused by working in ANALYSIS/.

2. Fixed errors related to paths and regular expressions

• Adjusted directory handling to prevent incorrect relative paths.
• Improved BAM file name parsing to avoid incorrect sample extraction.

3. Adapted _01_bam2fq.sh and _02_pgzip.sh to work properly

• _01_bam2fq.sh now correctly detects all BAM files in RAW/.
• _02_pgzip.sh ensures compression of FASTQ files and removes uncompressed files.

4. Created _03_symlink.sh to generate symbolic links in ANALYSIS/00-reads/

• Automatically removes broken links before recreating them.
• Ensures symlinks correctly point to RAW/*.fastq.gz instead of invalid paths.
• Uses ln -sf to force overwrite incorrect links if they exist.

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Execution Workflow

With these changes, the correct pipeline execution is:

bash lablog_bam2fq.sh   # Generates scripts
bash _01_bam2fq.sh      # Convert BAM to FASTQ in RAW/
bash _02_pgzip.sh       # Compress FASTQ 
bash _03_symlink.sh     # Create correct symbolic links in ANALYSIS/00-reads/

[svarona]

LGTM