niekwit/rna-seq-star-rmats

Snakemake workflow for splicing analysis of RNA-seq data using rMATS

Overview

Latest release: v0.1.0, Last update: 2026-07-22

Share link: https://snakemake.github.io/snakemake-workflow-catalog?wf=niekwit/rna-seq-star-rmats

Quality control: linting: passed formatting: failed

Wrappers: bio/fastqc bio/samtools/index bio/trim_galore/pe

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/niekwit/rna-seq-star-rmats . --tag v0.1.0

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.

Workflow overview

This workflow is a best-practice workflow for <detailed description>. The workflow is built using snakemake and consists of the following steps:

  1. Download genome reference from NCBI

  2. Validate downloaded genome (python script)

  3. Simulate short read sequencing data on the fly (dwgsim)

  4. Check quality of input read data (FastQC)

  5. Collect statistics from tool output (MultiQC)

Running the workflow

Input data

This template workflow creates artificial sequencing data in *.fastq.gz format. It does not contain actual input data. The simulated input files are nevertheless created based on a mandatory table linked in the config.yaml file (default: .test/samples.tsv). The sample sheet has the following layout:

sample

condition

replicate

read1

read2

sample1

wild_type

1

sample1.bwa.read1.fastq.gz

sample1.bwa.read2.fastq.gz

sample2

wild_type

2

sample2.bwa.read1.fastq.gz

sample2.bwa.read2.fastq.gz

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 sample sheet, mandatory

yes

config/samples.csv

genome

string

genome build (e.g. hg38, hg19, mm38, mm39)

yes

release

integer

Ensembl release number for genome/GTF retrieval

yes

raw_read_length

integer

read length of the raw (untrimmed) sequencing data

yes

star

yes

. index

yes

. . extra

string

extra arguments passed to STAR genomeGenerate

yes

. align

yes

. . extra

string

extra arguments passed to STAR alignReads

yes

rmats

yes

. lib_type

string

rMATS –libType value

yes

fr-unstranded

. extra

string

extra arguments passed to rmats.py

yes

. fdr

number

significance threshold used for plotting/summarising rMATS output

yes

0.05

. delta_psi

number

minimum

IncLevelDifference

used for plotting/summarising rMATS output

ngs_tracker

. enabled

boolean

set to false to skip NGS Tracker registration

yes

false

. base_url

string

NGS Tracker API base URL

. project_id

integer

NGS Tracker project ID

. run_id

integer

optional existing NGS Tracker run ID

. workflow_name

string

. workflow_tag

string

. workflow_system

string

. description

string

. tags

array

. files

array

Linting and formatting

Linting results
All tests passed!
Formatting results
 1[DEBUG] 
 2[DEBUG] In file "/tmp/tmp0uqawdoe/niekwit-rna-seq-star-rmats-1913ed8/workflow/rules/fastqc.smk":  Formatted content is different from original
 3[DEBUG] 
 4[DEBUG] In file "/tmp/tmp0uqawdoe/niekwit-rna-seq-star-rmats-1913ed8/workflow/Snakefile":  Formatted content is different from original
 5[DEBUG] 
 6[DEBUG] In file "/tmp/tmp0uqawdoe/niekwit-rna-seq-star-rmats-1913ed8/workflow/rules/mapping.smk":  Formatted content is different from original
 7[DEBUG] 
 8[DEBUG] In file "/tmp/tmp0uqawdoe/niekwit-rna-seq-star-rmats-1913ed8/workflow/rules/common.smk":  Formatted content is different from original
 9[DEBUG] 
10[DEBUG] 
11[DEBUG] In file "/tmp/tmp0uqawdoe/niekwit-rna-seq-star-rmats-1913ed8/workflow/rules/rmats.smk":  Formatted content is different from original
12[DEBUG] 
13[ERROR] In file "/tmp/tmp0uqawdoe/niekwit-rna-seq-star-rmats-1913ed8/workflow/rules/resources.smk":  InvalidParameterSyntax: 45"STAR "
14"--runThreadN {threads} "# Number of threads
15"--runMode genomeGenerate "# Indexation mode
16"--genomeFastaFiles {input.fasta} "# Path to fasta files
17"--sjdbOverhang {params.sjdbOverhang} "# Read-len - 1
18"--sjdbGTFfile {input.gtf} "
19"{params.extra} "# Optional parameters
20"--genomeDir {output} "# Path to output
21"> {log} 2>&1"# Logging
22[INFO] In file "/tmp/tmp0uqawdoe/niekwit-rna-seq-star-rmats-1913ed8/workflow/rules/resources.smk":  1 file(s) raised parsing errors 🤕
23[INFO] In file "/tmp/tmp0uqawdoe/niekwit-rna-seq-star-rmats-1913ed8/workflow/rules/resources.smk":  5 file(s) would be changed 😬
24[INFO] In file "/tmp/tmp0uqawdoe/niekwit-rna-seq-star-rmats-1913ed8/workflow/rules/resources.smk":  1 file(s) would be left unchanged 🎉
25
26snakefmt version: 0.11.5