exacto

Predict mutant proteoforms using Exacto

usage

nexus run --nf-workflow peptide_prediction_exacto.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 — peptide_prediction_exacto
#
# Usage:
#   nextflow run peptide_prediction_exacto.nf -params-file params.yaml
#
# Mirrors the exacto mutant-proteoform-prediction pipeline:
#   https://pirl-unc.github.io/exacto/pipelines/mutant-proteoform-prediction.html
# =============================================================================


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

# TSV file with the following columns (one row per sample):
#   sample_id
#   tumor_dna_fastq_file       long-read tumor  DNA fastq.gz
#   normal_dna_fastq_file      long-read normal DNA fastq.gz (matched control)
#   tumor_rna_fastq_file       long-read tumor  RNA fastq.gz
samples_tsv_file: ""

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

# Reference genome FASTA file (bgzipped is OK; exacto + samtools handle .gz)
reference_genome_fasta_file: ""

# Reference gene annotation file (e.g. GENCODE *.gtf.gz)
reference_gene_annotation_file: ""

# Reference gene annotation source / assembly / version (consumed by several
# exacto subcommands — keep these consistent with reference_gene_annotation_file)
reference_gene_annotation_source: "gencode"
reference_gene_annotation_assembly: "hg38"
reference_gene_annotation_version: "v45"

# Reference proteome FASTA file (e.g. GENCODE translations FASTA)
reference_proteome_fasta_file: ""


# -----------------------------------------------------------------------------
# Translation strategy
# -----------------------------------------------------------------------------
# Passed to `exacto translate-structs`.
#   'longest_orf' : translate only the longest ORF per transcript structure
#   'all_orfs'    : translate every ORF per transcript structure
strategy: "longest_orf"


# -----------------------------------------------------------------------------
# Read group tags (passed to minimap2 via -R "@RG\\t...")
# -----------------------------------------------------------------------------
platform_tag: "unknown"
platform_unit_tag: "unknown"
library_tag: "unknown"


# -----------------------------------------------------------------------------
# Per-tool extra CLI arguments
#
# Each field below is appended verbatim to the corresponding tool invocation.
# Defaults follow the exacto reference pipeline; leave fields empty ("") to
# skip extra args entirely.
# -----------------------------------------------------------------------------
exacto:
  # ---- minimap2 ----
  # Tumor + normal DNA alignment (PacBio HiFi preset)
  minimap2_dna_args: "-ax map-hifi --cs --eqx -Y -L --secondary=no"

  # Filtered transcript-assembly FASTA → genome alignment (long-read RNA preset)
  minimap2_rna_args: "-ax splice:hq -uf --cs --eqx -Y -L --secondary=no"

  # ---- RNA-Bloom2 (transcript assembly) ----
  # See: https://github.com/bcgsc/RNA-Bloom
  # Reference pipeline uses '-chimera -lrpb' for PacBio HiFi long-read input.
  rnabloom2_extra_args: "-chimera -lrpb"

  # ---- nexus_filter_rnabloom2_transcripts ----
  filter_rnabloom2_extra_args: ""

  # ---- exacto remove-unspliced-rnas ----
  remove_unspliced_rnas_extra_args: ""

  # ---- exacto call-rna-vars ----
  call_rna_vars_extra_args: ""

  # ---- exacto call-somatic-dna-vars ----
  # Set --preset to 'pb' (PacBio HiFi) or 'ont' (Oxford Nanopore) to match the
  # sequencing platform of the input DNA FASTQ files.
  call_somatic_dna_vars_extra_args: "--preset pb"

  # ---- exacto annotate-vars ----
  annotate_vars_extra_args: ""

  # ---- exacto integrate-vars ----
  integrate_vars_extra_args: ""

  # ---- exacto translate-structs ----
  translate_structs_extra_args: ""

  # ---- exacto call-peptide-vars ----
  call_peptide_vars_extra_args: ""