# =============================================================================
# params.yaml — quantification_long-read
#
# Usage:
#   nextflow run quantification_long-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               (required for bambu, liqa)
#   bam_bai_file           (required for bambu, liqa)
#   fastq_file             (required for kallisto, oarfish, transigner)
samples_tsv_file: ""

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

# Reference genome FASTA file (required for bambu)
reference_genome_fasta_file: ""

# Reference genes GTF file (required for bambu, kallisto, liqa)
reference_genes_gtf_file: ""

# Reference transcripts FASTA file (required for kallisto, oarfish, transigner)
reference_transcripts_fasta_file: ""


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

# Methods to run. Comma-separated list or 'all'.
# Allowed values:
#   all, bambu, kallisto, liqa, oarfish, transigner
methods: "all"


# -----------------------------------------------------------------------------
# Bambu
# No additional configuration required beyond reference files.
# -----------------------------------------------------------------------------
bambu: {}


# -----------------------------------------------------------------------------
# Kallisto (long-read mode)
# Optional arguments.
# -----------------------------------------------------------------------------
kallisto:
  # Extra CLI arguments passed directly to kallisto index.
  index_extra_args: "-k 63"

  # Extra CLI arguments passed directly to kallisto bus.
  bus_extra_args: "-x bulk --threshold 0.8"

  # Extra CLI arguments passed directly to bustools sort.
  bustools_sort_extra_args: ""

  # Extra CLI arguments passed directly to bustools count.
  bustools_count_extra_args: "--cm -m"

  # Extra CLI arguments passed directly to kallisto quant-tcc.
  quanttcc_extra_args: "-P PacBio --matrix-to-files"


# -----------------------------------------------------------------------------
# LIQA
# Optional arguments.
# -----------------------------------------------------------------------------
liqa:
  # Extra CLI arguments passed directly to liqa quantify.
  extra_args: "-max_distance 20 -f_weight 1"


# -----------------------------------------------------------------------------
# Oarfish
# Optional arguments.
# -----------------------------------------------------------------------------
oarfish:
  # Extra CLI arguments passed directly to oarfish.
  extra_args: "--seq-tech pac-bio-hifi"


# -----------------------------------------------------------------------------
# TranSigner
# Optional arguments.
# -----------------------------------------------------------------------------
transigner:
  # Extra CLI arguments passed directly to transigner align.
  align_extra_args: ""

  # Extra CLI arguments passed directly to transigner prefilter.
  prefilter_extra_args: ""

  # Extra CLI arguments passed directly to transigner em.
  em_extra_args: ""