TRON-Bioinformatics/oblx

Reproducible generation of references and resources for next generation sequencing pipelines.

Overview

Latest release: v1.0.0, Last update: 2026-06-18

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

Quality control: linting: failed formatting: passed

Topics: ngs-analysis reproducible-research snakemake-workflow snakemake oblx workflow

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/oblx . --tag v1.0.0

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

To run the workflow using a combination of conda and apptainer/singularity for software deployment, use

snakemake --cores all --sdm conda apptainer

To run the workflow with automatic deployment of all required software via conda/mamba, use

snakemake --cores all --sdm conda

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.

Configuration

See the config section in our online docs.

Workflow parameters

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

Parameter

Type

Description

Required

Default

organism

string

Trivial name of the organism for which the genomelib should be built.

human

genome_build

string

GRC reference genome build for which the genomelib should be built.

GRCh38

release

string

Release number of the GENCODE annotation for the corresponding reference genome_build.

49

gnomad_release

string

Release number of the gnomAD resources to be used.

4.1

intron_slop

integer

Number of intronic bases that should extend the exome definition ref_exome.bed.

20

exome_transcript_definition

string

Define which GENCODE transcripts should be used to create the exome definition. The default is the "basic" tag. Please note that GENCODE basic definitions were deprecated in version 48 and replaced by the tag "GENCODE_Primary". These are not the same sets of transcripts. For now, we recommend continuing to use basic transcripts.

basic

star_sjdb_overhang

integer

--sjdbOverhang parameter for STAR index generation (should be read length - 1, in most cases 100 should be sufficient).

100

star_genome_sa_index_n_bases

integer

Defines the STAR parameter genomeSAindexNbases. The lower the value, the smaller the index. This can be useful, when creating test data for CI tests to keep the file small.

14

minimum_allele_frequency

number

af_only_gnomad_hg38.vcf.gz variants are filtered for population allele frequency above this cutoff. Only needed when organism is “human”.

0.001

gencode_url

string

URL from which GENCODE resources can be downloaded. Expected to point to the root of a FTP directory (accessed via HTTPS) under which the general GENCODE dir structure can be found, i.e., /Gencode_/release_/.

https://ftp.ebi.ac.uk/pub/databases/gencode

ucsc_url

string

URL from which UCSC resources can be downloaded. Expected to point to the root of a directory (accessed via HTTPS) under which the UCSC “problematic”, “exomeProbesets”, and “gencode” bigBed resource files may be found. Only needed when organism is “human”.

https://hgdownload.soe.ucsc.edu/gbdb/hg38

ucsc_golden_path_url

string

URL from which the UCSC golden path resources (i.e. the repeatmasking resource file) can be downloaded for a given assembly. Only needed when organism is “human”.

https://hgdownload.soe.ucsc.edu/goldenPath

gatk_url

string

URL from which the GATK resources may be downloaded. Only needed when organism is “human”.

https://storage.googleapis.com/gcp-public-data–broad-references/hg38/v0

gnomad_url

string

URL from which the gnomAD population SNP VCF files may be downloaded. Only needed when organism is “human”.

https://storage.googleapis.com/gcp-public-data–gnomad/release

chrom_filter

array

List of chromosome names to be included in the genomelib. Only needed when organism is “human” as this currently only defines which chromosomes are downloaded from gnomAD (chrM is not included at the moment as this would require to download from gnomAD v3.1).

[‘chr1’, ‘chr2’, ‘chr3’, ‘chr4’, ‘chr5’, ‘chr6’, ‘chr7’, ‘chr8’, ‘chr9’, ‘chr10’, ‘chr11’, ‘chr12’, ‘chr13’, ‘chr14’, ‘chr15’, ‘chr16’, ‘chr17’, ‘chr18’, ‘chr19’, ‘chr20’, ‘chr21’, ‘chr22’, ‘chrX’, ‘chrY’]

Linting and formatting

Linting results
1Using workflow specific profile workflow/profiles/default for setting default command line arguments.
2WorkflowError in file "/tmp/tmpwt6gxj5n/TRON-Bioinformatics-oblx-2651959/workflow/Snakefile", line 14:
3Expecting Snakemake version 9.20.0 or higher (you are currently using 9.17.2).
Formatting results
All tests passed!