inputs_allvall_example.yml

# Sample Input File for All-vs-All Comparison
#
# This example shows how to run the sample matching workflow in
# all-vs-all mode (comparing every BAM file against every other BAM file).
#
# Usage:
#   cwltool main.cwl inputs_allvall_example.yml

bam_directory:
  class: Directory
  path: test/bam
  # Replace with the actual path to your directory containing BAM files
  # The directory can contain subdirectories - the workflow will scan recursively

# pairs_csv is omitted - this triggers all-vs-all mode
# When pairs_csv is not provided, Picard CrosscheckFingerprints will compare
# all samples against each other in a single run

reference_genome:
  class: File
  path: test/genome.fasta
  # Reference genome in FASTA format
  # Example: hg38.fasta, GRCh38.fasta, etc.

haplotype_map:
  class: File
  path: test/haplotype_map.txt
  # Haplotype map file required by Picard
  # Available from Broad Institute:
  # https://github.com/broadinstitute/picard/tree/master/src/main/resources/picard/fingerprint

# regex_split: "[_\\.]"
# Optional: Regular expression pattern to split BAM filenames for sample name extraction
# If not provided, uses basename (everything before .bam extension)
# Common patterns:
#   "[_\\.]"  - Split on underscore or dot
#   "_"       - Split only on underscore
#   "\\."     - Split only on dot
#   "-"       - Split on hyphen
# Example: For "Sample123_L001.bam" with regex "[_\\.]"
#          Sample name will be "Sample123"
# Example: For "Sample123_L001.bam" without regex_split
#          Sample name will be "Sample123_L001"

# cpu: 16
# Optional: Number of CPU cores to allocate for crosscheck_fingerprints step
# Default: 16 cores

# ram: 38000
# Optional: Amount of RAM in MiB to allocate for crosscheck_fingerprints step
# Default: 38000 MiB (38 GB)
# Increase if you get out-of-memory errors with large datasets