# =============================================================================
# params.yaml — assembly_short-read-rna
#
# Usage:
#   nextflow run assembly_short-read-rna.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
#   fastq_file_1    (paired-end read 1, for spades and trinity)
#   fastq_file_2    (paired-end read 2, for spades and trinity)
#   bam_file        (splice-aware aligned reads, e.g. STAR/HISAT2, for bookend)
#   bam_bai_file    (index of bam_file, for bookend)
samples_tsv_file: ""

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

# Reference genome FASTA file (reference-guided assembly)
# Required when methods includes 'bookend' or 'all'.
reference_genome_fasta_file: ""


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

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


# -----------------------------------------------------------------------------
# rnaSPAdes (de novo, paired-end FASTQ)
# Optional arguments.
# -----------------------------------------------------------------------------
spades:
  # Extra CLI arguments passed directly to rnaspades.py.
  # (-1/-2/-o/-t/-m are supplied by the workflow.)
  extra_args: ""


# -----------------------------------------------------------------------------
# Trinity (de novo, paired-end FASTQ)
# Optional arguments.
# -----------------------------------------------------------------------------
trinity:
  # Extra CLI arguments passed directly to Trinity.
  # (--seqType/--left/--right/--output/--CPU/--max_memory are supplied by the workflow.)
  extra_args: ""


# -----------------------------------------------------------------------------
# Bookend (reference-guided, aligned BAM)
# Optional arguments.
# -----------------------------------------------------------------------------
bookend:
  # Extra CLI arguments passed directly to `bookend assemble`.
  params_assemble: ""

  # Extra CLI arguments passed directly to `bookend fasta`.
  params_fasta: ""