Isoform Characterization (Long-read)

Characterize isoforms in long-read RNA sequencing BAM/FASTQ files

tools

The following tools run by default (methods: "all"):

espresso, flair, isoquant, isotools, mandalorion, sqanti3-gtf, talon

usage

nexus run --nf-workflow isoform_characterization_long-read.nf -params-file params.yaml

Note

Nextflow config files are available here. Use the config file that matches your installed nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

parameters

Download params.yaml

# =============================================================================
# params.yaml — isoform_characterization_long-read
#
# Usage:
#   nextflow run isoform_characterization_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 ESPRESSO, IsoTools, TALON)
#   bam_bai_file           (required for ESPRESSO, IsoTools, TALON)
#   fastq_file             (required for FLAIR, IsoQuant, Mandalorion)
samples_tsv_file: ""

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

# Reference genome FASTA file
reference_genome_fasta_file: ""

# Reference genes GTF file
reference_genes_gtf_file: ""


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

# Methods to run. Comma-separated list or 'all'.
# Allowed values:
#   all, espresso, flair, isoquant, isotools, mandalorion,
#   sqanti3-gtf, talon
methods: "all"


# -----------------------------------------------------------------------------
# ESPRESSO
# Optional arguments.
# -----------------------------------------------------------------------------
espresso:
  # Extra CLI arguments passed directly to ESPRESSO_S.pl.
  s_extra_args: ""

  # Extra CLI arguments passed directly to ESPRESSO_C.pl.
  c_extra_args: ""

  # Extra CLI arguments passed directly to ESPRESSO_Q.pl.
  q_extra_args: ""


# -----------------------------------------------------------------------------
# FLAIR
# Optional arguments.
# -----------------------------------------------------------------------------
flair:
  # Extra CLI arguments passed directly to flair align.
  align_extra_args: ""

  # Extra CLI arguments passed directly to flair correct.
  correct_extra_args: ""

  # Extra CLI arguments passed directly to flair collapse.
  collapse_extra_args: ""


# -----------------------------------------------------------------------------
# IsoQuant
# Optional arguments.
# -----------------------------------------------------------------------------
isoquant:
  # Extra CLI arguments passed directly to isoquant.
  extra_args: "--data_type pacbio_ccs --sqanti_output --high_memory --complete_genedb"


# -----------------------------------------------------------------------------
# IsoTools
# Optional arguments.
# -----------------------------------------------------------------------------
isotools:
  # Extra CLI arguments passed directly to isotools.
  extra_args: ""


# -----------------------------------------------------------------------------
# Mandalorion
# Optional arguments.
# -----------------------------------------------------------------------------
mandalorion:
  # Extra CLI arguments passed directly to Mandalorion.
  extra_args: ""


# -----------------------------------------------------------------------------
# SQANTI3 (GTF mode)
# Runs on GTF outputs from upstream tools (ESPRESSO, FLAIR, IsoQuant,
# IsoTools, Mandalorion).
# Optional arguments.
# -----------------------------------------------------------------------------
sqanti3_gtf:
  # Extra CLI arguments passed directly to sqanti3_qc.py.
  qc_extra_args: "--report skip"

  # Extra CLI arguments passed directly to sqanti3_filter.py.
  filter_extra_args: "ml --skip_report"


# -----------------------------------------------------------------------------
# TALON
# Optional arguments.
# -----------------------------------------------------------------------------
talon:
  # Extra CLI arguments passed directly to talon_initialize_database.
  initdb_extra_args: ""

  # Extra CLI arguments passed directly to talon.
  extra_args: "--create_novel_spliced_genes"