Validate and launch bioinformatics workflows

Validate inputs and execute matched tumor-normal variant calling

Reproducible tumor-normal variant calling when validation and artifact generation must precede execution.

• · Tumor BAM file
• · Normal BAM file
• · Patient/sample IDs
• · Output directory
• · Reference (--fasta or --genome)

• · Pacsomatic samplesheet
• · Params YAML
• · Launch script
• · Nextflow job ID (if executed)

• · nf-core/pacsomatic pipeline
• · Nextflow
• · Singularity/Docker
• · LSF/Slurm/PBS/SGE scheduler (optional)

Valid BAM files with indices, Nextflow/Singularity installed, reference genome available

Invalid BAM file paths, missing reference genome, scheduler submission fails, Nextflow execution error

• · Single entrypoint (run_pacsomatic.py)
• · Dry-run validation before execution
• · Reproducible params YAML and launch script generation