# =============================================================================
# params.yaml — isoform_characterization_short-read
#
# Usage:
#   nextflow run isoform_characterization_short-read.nf -params-file params.yaml
#
# Fill in the required fields below. Optional fields can be left at their
# defaults or removed entirely.
# =============================================================================


# -----------------------------------------------------------------------------
# Required
# -----------------------------------------------------------------------------

# TSV file with columns:
#   sample_id
#   bam_file
#   bam_bai_file
samples_tsv_file: ""

# Directory to which output files will be copied
output_dir: ""

# Reference genes GTF file
reference_genes_gtf_file: ""


# -----------------------------------------------------------------------------
# Optional — general
# -----------------------------------------------------------------------------

# Methods to run. Comma-separated list or 'all'.
# Allowed values:
#   all, rmats
methods: "all"


# -----------------------------------------------------------------------------
# rMATS
# Optional arguments.
# -----------------------------------------------------------------------------
rmats:
  # Extra CLI arguments passed directly to rmats.py.
  extra_args: "-t paired --libType fr-unstranded --readLength 151"