This Nextflow workflow runs ichorCNA on all the samples listed in the input sample sheet located under the data/ folder.

Each row in the sample sheet should correspond to a unique sample, with the following fields specified:

• Path to the input tumor BAM file.
• A unique SAMPLEID for each sample.

Configuration Please update the following parameters in your nextflow.config file:

Output Directory Set the outdir parameter to define where output files will be saved. A new subfolder per sample will be created within this directory.

Reference Genome Parameters Adjust based on the reference genome you're using:

chrs genomeStyle genomeBuild Defaults are set for GIAB hg38.

WIG and Centromere Files Update the paths to the following:

gcWig mapWig repTimeWig (optional) centromere Defaults are also based on GIAB hg38.

Outputs The pipeline produces the following: All copy number output files from the optimal solution. A combined figure: genomeWide_all_solutions.pdf showing results across all solutions. Subdirectories for each solution (normal, ploidy combinations) under the sample output folder.

To Run: bash run_pipeline.sh