AllenInstitute/Bulk-RNA-Snakeline

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Overview

Latest release: None, Last update: 2026-07-13

Share link: https://snakemake.github.io/snakemake-workflow-catalog?wf=AllenInstitute/Bulk-RNA-Snakeline

Quality control: linting: failed formatting: passed

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/AllenInstitute/Bulk-RNA-Snakeline . --tag None

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 4: Run workflow

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

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

Copy config/config.yaml and config/samples.csv before changing them. Pass the copied configuration to Snakemake with --configfile.

Sample sheet

The sample sheet is a comma-separated CSV file with three columns:

Column	Meaning
`sample`	A unique name containing letters, numbers, periods, underscores, or hyphens.
`read1`	Path to the gzipped R1 FASTQ file.
`read2`	Path to the matching gzipped R2 FASTQ file.

Paths may be absolute or relative to the directory where Snakemake runs. The workflow reads input files where they are. It never moves or renames them.

Reference files

Set reference.fasta to the genome FASTA and reference.annotation to its matching GTF file. Set reference.read_length to the number of bases in each read before trimming. The workflow passes read_length - 1 to STAR as sjdbOverhang when it builds an index.

Leave reference.star_index as null to build an index. To reuse an index, set it to the index directory. That directory must contain genomeParameters.txt and must have been built from the same FASTA and GTF with a compatible STAR version.

Library direction

Set library.strandedness to:

forward for StringTie --fr
reverse for StringTie --rf
unstranded to omit a direction flag

Confirm this value with the library preparation protocol. A wrong value changes transcript quantification.

Resources

Each step has threads, memory_mb, and runtime_minutes settings. Snakemake uses them when it schedules jobs. Start with the defaults, then adjust them from observed run times and peak memory on your data.

Workflow parameters

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

Parameter	Type	Description	Required
samples	string	Path to the comma-separated sample sheet.	yes
results_dir	string	Output directory, relative to the working directory.	yes
reference			yes
. fasta	string		yes
. annotation	string		yes
. star_index	[‘string’, ‘null’]		yes
. read_length	integer		yes
library			yes
. strandedness			yes
trimming			yes
. forward_adapter	string		yes
. reverse_adapter	string		yes
. trim_front	integer		yes
. minimum_length	integer		yes
. minimum_quality	integer		yes
resources			yes
. cutadapt			yes
. fastqc			yes
. star_index			yes
. star_align			yes
. stringtie			yes
. multiqc			yes

Linting and formatting

Linting results

WorkflowError in file "/tmp/tmp_1dnp3dl/workflow/Snakefile", line 11:
Workflow defines configfile ../config/config.yaml but it is not present or accessible (full checked path: /tmp/config/config.yaml).