05. Config File

This file contains all parameters for each step of the workflow.

User

In the config/config.yaml, change the User specific values, including the cancer cell type.

# Change those values to yours
User:
  input_dir: /path/to/input_dir
  output_dir: /path/to/output_dir
  sample_map: /path/to/sample_map.tsv
  cancer_cell_type: HGSOC

Run

You can run different pipeline parts depending on your needs by changing values in the Run section:

# Change any of those to True if you want to run it, else False
Run:
  # Create a PoN based on normal samples (facultative)
  PoN: False
  # Run cell type reannotation
  CellTypeReannotation: True
  # Run SNV calling with SComatic
  SNVCalling: True
  # Run cell clustering with BnpC
  CellClustering: True
  # Run fusion calling with CTAT-LR-Fusion
  FusionCalling: True
  # Run CNV calling with InferCNV
  CNACalling: False

By default, we recommend running CellTypeReannotation, SNVCalling, FusionCalling, and CellClustering. Note that CellTypeReannotation will call SNVs and fusions to reannotate cells, while SNVCalling and FusionCalling will "redo" the somatic variants calling based on reannotated cell types.

Reference

By default, LongSom uses the installed reference in ref/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/ that needs to be downloaded as reference (see Install Wiki). Users can instead define their own reference by setting an absolute path in config/config.yaml instead of:

# Change if you use a custom reference
Reference:
  genome: ../ref/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa
  isoforms: ../ref/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf
  gnomAD_db: ../ref/gnomAD_v4.1

Others

All available parameters are present in the config file and can be changed there.