ylab-hi/ScanNeo2

Snakemake-based computational workflow for neoantigen prediction from diverse sources

Overview

Latest release: v0.3.7, Last update: 2025-11-01

Linting: linting: failed, Formatting: formatting: failed

Topics: epitope gene-fusion indels neoantigens peptide snakemake snakemake-workflow splicing exitron neoepitope immunotherapy vaccine

Wrappers: bio/arriba bio/bowtie2/align bio/bowtie2/build bio/bwa/index bio/fastp bio/fastqc bio/gatk/applybqsr bio/gatk/applyvqsr bio/gatk/baserecalibrator bio/gatk/filtermutectcalls bio/gatk/haplotypecaller bio/gatk/mutect bio/gatk/selectvariants bio/gatk/variantrecalibrator bio/picard/createsequencedictionary bio/samtools/faidx bio/samtools/index bio/samtools/merge bio/star/align bio/star/index bio/tabix/index bio/vep/annotate

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Conda. 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/ylab-hi/ScanNeo2 . --tag v0.3.7

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.

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.

General Configuration

Configure ScanNeo2 by editing the config/config.yml file. Make sure to adjust parameters to suit your needs and data. Note that the paths in the config file need to be relative to the directory from which you run snakemake.

For a detailed description of the parameters, please refer to section about the configuration in the wiki. Different locations of configuration files can be specified using --configfile config.yaml.

Linting and formatting

Linting results

1IndexError in file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/common.smk", line 64:
2list index out of range
3  File "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/common.smk", line 126, in <module>
4  File "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/common.smk", line 8, in data_structure
5  File "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/common.smk", line 64, in handle_seqfiles

Formatting results

 1[DEBUG] 
 2[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/exitron.smk":  Formatted content is different from original
 3[DEBUG] 
 4[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/prelim.smk":  Formatted content is different from original
 5[DEBUG] 
 6[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/altsplicing.smk":  Formatted content is different from original
 7[DEBUG] 
 8[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/genefusion.smk":  Formatted content is different from original
 9[DEBUG] 
10[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/Snakefile":  Formatted content is different from original
11[DEBUG] 
12[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/quantification.smk":  Formatted content is different from original
13[DEBUG] 
14[ERROR] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/germline.smk":  InvalidParameterSyntax: 176resources={
15"hapmap": {"known": False , "training": True , "truth": True , "prior": 15.0} ,
16"omni": {"known": False , "training": True , "truth": True , "prior": 12.0} ,
17"g1k": {"known": False , "training": True , "truth": True , "prior": 10.0} ,
18
19[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/germline.smk":  
20[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/align.smk":  Formatted content is different from original
21[DEBUG] 
22[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/annotation.smk":  Formatted content is different from original
23[DEBUG] 
24[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/hlatyping_mhcII.smk":  Formatted content is different from original
25[DEBUG] 
26[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/hlatyping_mhcI.smk":  Formatted content is different from original
27[DEBUG] 
28[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/preproc.smk":  Formatted content is different from original
29[DEBUG] 
30[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/hlatyping_prep.smk":  Formatted content is different from original
31[DEBUG] 
32[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/custom.smk":  Formatted content is different from original
33[DEBUG] 
34[ERROR] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/common.smk":  InvalidPython: Black error:

Cannot parse for target version Python 3.13: 66:0: else:

(Note reported line number may be incorrect, as snakefmt could not determine the true line number)


[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/common.smk":  
[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/indel.smk":  Formatted content is different from original
[DEBUG] 
[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/prioritization.smk":  Formatted content is different from original
[DEBUG] 
[DEBUG] In file "/tmp/tmpz0gxn349/ylab-hi-ScanNeo2-a9abaf8/workflow/rules/ref.smk":  Formatted content is different from original
[INFO] 2 file(s) raised parsing errors 🤕
[INFO] 16 file(s) would be changed 😬

snakefmt version: 0.11.2