mopepgen-gencode

Predict mutant peptide sequences using moPepGen

usage

nexus run --nf-workflow peptide_prediction_mopepgen-gencode.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_mopepgen-gencode
#
# Usage:
#   nextflow run peptide_prediction_mopepgen-gencode.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               (required)
#   *_vcf_file              (any column ending in _vcf_file is auto-discovered
#                            as a VEP-based VCF input; the prefix becomes the
#                            variant source label, e.g. mutect2_vcf_file -> mutect2)
#   reditools2_tsv_file     (optional, use 'NA' or empty to skip)
#   arriba_tsv_file         (optional, use 'NA' or empty to skip)
#   rmats_output_dir        (optional, use 'NA' or empty to skip)
#   circexplorer2_bed_file  (optional, use 'NA' or empty to skip)
samples_tsv_file: ""

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

# Reference genome FASTA file (GENCODE)
reference_genome_fasta_file: ""

# Reference genes GTF file (GENCODE)
reference_genes_gtf_file: ""

# Reference proteome FASTA file (GENCODE)
reference_proteome_fasta_file: ""


# -----------------------------------------------------------------------------
# VEP
# -----------------------------------------------------------------------------
vep:
  # VEP cache directory
  dir: ""

  # Extra CLI arguments passed directly to VEP.
  extra_args: "--species homo_sapiens --offline --cache --assembly GRCh38 --distance 0"

  # Extra CLI arguments passed directly to filter_vep.
  filter_extra_args: "--filter Source = GENCODE"

  # Reference source label used by VEP custom annotation and moPepGen.
  reference_source: "GENCODE"


# -----------------------------------------------------------------------------
# moPepGen
# -----------------------------------------------------------------------------
mopepgen:
  # Extra CLI arguments passed directly to moPepGen parseVEP.
  parsevep_extra_args: "--skip-failed"

  # Extra CLI arguments passed directly to moPepGen parseREDItools.
  parsereditools_extra_args: ""

  # Extra CLI arguments passed directly to moPepGen parseArriba.
  parsearriba_extra_args: "--skip-failed"

  # Extra CLI arguments passed directly to moPepGen parseRMATS.
  parsermats_extra_args: ""

  # Extra CLI arguments passed directly to moPepGen parseCIRCexplorer.
  parsecircexplorer2_extra_args: "--skip-failed"

  # Extra CLI arguments passed directly to moPepGen callVariant.
  callvariant_extra_args: ""