TRON-Bioinformatics/neorasp

NEOantigens from RNa-SPlicing

Overview

Latest release: v0.6.0, Last update: 2026-07-02

Share link: https://snakemake.github.io/snakemake-workflow-catalog?wf=TRON-Bioinformatics/neorasp

Quality control: linting: failed formatting: passed

Topics: rna-seq snakemake splicing-derived-neoepitopes

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Conda package manager. It is recommended to install conda via Miniforge. Run

conda create -c conda-forge -c bioconda -c nodefaults --name snakemake snakemake snakedeploy

to install both Snakemake and Snakedeploy in an isolated environment. For all following commands ensure that this environment is activated via

conda activate snakemake

For other installation methods, refer to the Snakemake and Snakedeploy documentation.

Step 2: Deploy workflow

With Snakemake and Snakedeploy installed, the workflow can be deployed as follows. First, create an appropriate project working directory on your system and enter it:

mkdir -p path/to/project-workdir
cd path/to/project-workdir

In all following steps, we will assume that you are inside of that directory. Then run

snakedeploy deploy-workflow https://github.com/TRON-Bioinformatics/neorasp . --tag v0.6.0

Snakedeploy will create two folders, workflow and config. The former contains the deployment of the chosen workflow as a Snakemake module, the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs.

Step 3: Configure workflow

To configure the workflow, adapt config/config.yml to your needs following the instructions below.

Step 4: Run workflow

The deployment method is controlled using the --software-deployment-method (short --sdm) argument.

To run the workflow using apptainer/singularity, use

snakemake --cores all --sdm apptainer

Snakemake will automatically detect the main Snakefile in the workflow subfolder and execute the workflow module that has been defined by the deployment in step 2.

For further options such as cluster and cloud execution, see the docs.

Step 5: Generate report

After finalizing your data analysis, you can automatically generate an interactive visual HTML report for inspection of results together with parameters and code inside of the browser using

snakemake --report report.zip

Configuration

The following section is imported from the workflow’s config/README.md.


# Input file section
sample_sheet: 'tests/pep/samples.tsv'
# Reference genome
reference:
  genome: 'tests/resources/GRCh38v45_minigenome/ref_genome.fa'
  annotation: 'tests/resources/GRCh38v45_minigenome/ref_annot.gtf'
  annotation_bed: 'tests/resources/GRCh38v45_minigenome/ref_annot.bed'
  cdna: 'tests/resources/GRCh38v45_minigenome/ref_cdna.fa'
  chromsizes: 'tests/resources/GRCh38v45_minigenome/ref_genome.chrom.sizes'
  encode_mapability: 'tests/resources/GRCh38v45_minigenome/mappability/encode_blacklist.bed'
  ucsc_mapability: 'tests/resources/GRCh38v45_minigenome/mappability/ucsc_unusal.bed'
  ref_transcripts: 'tests/resources/GRCh38v45_minigenome/ref_transcripts.RDS'
  ref_cds: 'tests/resources/GRCh38v45_minigenome/ref_cds.RDS'
  tx2gene: 'tests/resources/GRCh38v45_minigenome/tx2gene.tsv'
  gene2symbol: 'tests/resources/GRCh38v45_minigenome/hgnc2ensembl_id.tsv.gz'
  2bit: 'tests/resources/GRCh38v45_minigenome/ref_genome.2bit'
  canonical_juncs: tests/resources/GRCh38v45_minigenome/canonical_junctions.tsv
  rmsk: tests/resources/GRCh38v45_minigenome/ref_rmsk.Rds

# Tool configuration
fraser:
  min_read: 5
  mapq_filter: 255

star:
  min_read: 5
  ref: tests/resources/GRCh38v45_minigenome/indices/star

requantify:
  interval_mode: true
  allow_mismatches: false
  bowtie_k_threshold: 200
  cts_size: 1000

reliable_calls:
  min_junction_usage: 0.01
  min_junction_cpm: 0.1

splice2neo:
  peptide_flank_size: 13

Workflow parameters

The following table is automatically parsed from the workflow’s config.schema.y(a)ml file.

Parameter

Type

Description

Required

Default

sample_sheet

string

Path to the sample sheet TSV file

tests/pep/samples.tsv

reference

Paths to reference genome library files

{}

. genome

string

Path to the reference genome FASTA file

tests/resources/tron_genome_lib/resources/ref_genome.fasta

. annotation

string

Path to the gene annotation GTF file

tests/resources/tron_genome_lib/resources/ref_annot.gtf

. annotation_bed

string

Path to the gene annotation BED file

tests/resources/tron_genome_lib/resources/ref_annot.bed

. cdna

string

Path to the reference cDNA FASTA file

tests/resources/tron_genome_lib/resources/ref_transcripts.fasta

. chromsizes

string

Path to the chromosome sizes file

tests/resources/tron_genome_lib/resources/ref_genome.chrom.sizes

. encode_mapability

string

Path to the ENCODE blacklist BED file for mappability filtering

tests/resources/tron_genome_lib/resources/mappability/encode_exclusion.bed

. ucsc_mapability

string

Path to the UCSC unusual regions BED file for mappability filtering

tests/resources/tron_genome_lib/resources/mappability/ucsc_problematic.bed

. ref_transcripts

string

Path to the reference transcripts RDS file

tests/resources/tron_genome_lib/indices/R/ref_transcripts.Rds

. ref_cds

string

Path to the reference CDS RDS file

tests/resources/tron_genome_lib/indices/R/ref_cds.Rds

. tx2gene

string

Path to the transcript-to-gene mapping TSV file

tests/resources/tron_genome_lib/resources/ref_annot_transcript2gene.tsv

. gene2symbol

string

Path to the gene-to-symbol (HGNC to Ensembl) mapping file

tests/resources/tron_genome_lib/resources/ref_annot_gene2symbol.tsv2

. 2bit

string

Path to the reference genome 2bit file

tests/resources/tron_genome_lib/indices/R/ref_genome.2bit

. canonical_juncs

string

Path to the canonical junctions TSV file

tests/resources/tron_genome_lib/resources/ref_annot_splice_sites.tsv

. rmsk

string

Path to the RepeatMasker RDS file

tests/resources/tron_genome_lib/resources/ref_rmsk.Rds

fraser

FRASER splice junction detection configuration

{}

. min_read

integer

Minimum read count threshold

2

. mapq_filter

integer

Mapping quality filter value (0-255)

255

star

STAR aligner configuration

{}

. ref

string

Path to the STAR index directory

tests/resources/tron_genome_lib/indices/star

requantify

easyquant re-quantification configuration

{}

. interval_mode

boolean

Enable interval mode for re-quantification

true

. allow_mismatches

boolean

Allow mismatches during re-quantification alignment

false

. bowtie_k_threshold

integer

Bowtie k threshold for reporting multi-mapping reads

200

. cts_size

integer

Context sequence size in base pairs around the splice junction

1000

splice2neo

Splice2Neo peptide annotation configuration

{}

. peptide_flank_size

integer

Amino acid flank size around the splice junction for peptide generation

13

. scatter_size

integer

Number of junctions per scatter job for parallelisation

1000

reliable_calls

Thresholds for filtering reliable splice junction calls

{}

. min_junction_usage

number

Minimum junction usage ratio (proportion of reads spanning the junction)

0.01

. min_junction_cpm

number

Minimum junction expression in counts per million (CPM)

0.1

stringtie

StringTie transcript assembly configuration

{}

. min_junc_count

integer

Minimum number of spliced reads supporting a junction

1

. min_junc_anchor

integer

Minimum anchor length on either side of a junction

8

max_ass_distance

integer

Maximum distance (bp) for classifying a junction as an alternative splice site (ASS) rather than a deep intronic splice variant

50

Linting and formatting

Linting results
1Using workflow specific profile workflow/profiles/default for setting default command line arguments.
2ModuleNotFoundError in file "/tmp/tmp05sie27j/TRON-Bioinformatics-neorasp-3650640/workflow/rules/common.smk", line 2:
3No module named 'magic'
4  File "/tmp/tmp05sie27j/TRON-Bioinformatics-neorasp-3650640/workflow/rules/common.smk", line 2, in <module>
Formatting results
All tests passed!