Variant Calling (Long-read RNA)

Identify RNA variants and gene fusions in long-read RNA samples

tools

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

clair3rna, de-souza, longgf, pbfusion

usage

nexus run --nf-workflow variant_calling_long-read-rna.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 — variant_calling_long-read-rna
#
# Usage:
#   nextflow run variant_calling_long-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
#   bam_file        (minimap2-aligned, for clair3rna, longgf, pbfusion)
#   bam_bai_file    (minimap2-aligned, for clair3rna, longgf, pbfusion)
#   fastq_file      (raw reads, for de-souza)
samples_tsv_file: ""

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

# Reference genome FASTA file (for clair3rna, de-souza, pbfusion)
reference_genome_fasta_file: ""

# Reference genes annotation GTF file
# Required when methods includes 'longgf', 'pbfusion', or 'all'.
reference_genes_gtf_file: ""


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

# Methods to run. Comma-separated list or 'all'.
# Allowed values:
#   all, clair3rna, de-souza, longgf, pbfusion
methods: "all"


# -----------------------------------------------------------------------------
# Clair3-RNA
# Optional arguments.
# -----------------------------------------------------------------------------
clair3rna:
  # Extra CLI arguments passed directly to Clair3-RNA.
  extra_args: "--platform hifi_sequel2_minimap2"


# -----------------------------------------------------------------------------
# de Souza (lrRNAseqVariantCalling)
# Required when methods includes 'de-souza' or 'all':
#   deepvariant_input_path, deepvariant_output_path
# Optional otherwise.
# -----------------------------------------------------------------------------
de_souza:
  # Required when running de-souza (DeepVariant container bind-mount paths)
  deepvariant_input_path: ""
  deepvariant_output_path: ""

  # Extra CLI arguments passed directly to minimap2.
  params_minimap2: "-ax splice -uf -C5 --secondary=no"

  # Extra CLI arguments passed directly to samtools view.
  params_samtools_view: "-F 2308"

  # Read group tags
  platform_tag: "unknown"
  platform_unit_tag: "unknown"
  library_tag: "unknown"

  # DeepVariant containerization engine: 'singularity' or 'docker'
  deepvariant_containerization: "singularity"

  # DeepVariant --model_type value
  deepvariant_model_type: "PACBIO"

  # Path to the run_deepvariant binary
  deepvariant_bin_path: "/opt/deepvariant/bin/run_deepvariant"

  # DeepVariant version
  deepvariant_bin_version: "1.6.1"


# -----------------------------------------------------------------------------
# LongGF
# Optional arguments.
# -----------------------------------------------------------------------------
longgf:
  # Parameters passed directly to LongGF:
  #   <min-overlap-len> <bin_size> <min-map-len> [pseudogene:0(default)/1/other(no filter)] [Secondary_alignment:0(default)] [min_sup_read:2(default)] [output_flag:0]
  extra_args: "100 30 100 1 0 2 1"


# -----------------------------------------------------------------------------
# pbfusion
# Optional arguments.
# -----------------------------------------------------------------------------
pbfusion:
  # Extra CLI arguments passed directly to pbfusion discover.
  extra_args: "--min-coverage 3 --min-mean-mapq 20 --gtf-transcript-allow-lncRNA"