epigen/enrichment_analysis
A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.
Overview
Topics: bioinformatics genomic-regions enrichment-analysis atac-seq biomedical-data-science chip-seq gene-set-enrichment gene-sets rna-seq visualization pipeline snakemake workflow motif-enrichment-analysis
Latest release: v2.0.0, Last update: 2024-12-19
Linting: linting: failed, Formatting:formatting: failed
Deployment
Step 1: Install Snakemake and Snakedeploy
Snakemake and Snakedeploy are best installed via the Mamba package manager (a drop-in replacement for conda). If you have neither Conda nor Mamba, it is recommended to install Miniforge. More details regarding Mamba can be found here.
When using Mamba, run
mamba create -c conda-forge -c bioconda --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
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/epigen/enrichment_analysis . --tag v2.0.0
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 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
.
You need one configuration file and one annotation file to run the complete workflow. You can use the provided example as starting point. If in doubt read the comments in the config and/or try the default values.
- project configuration (config/config.yaml): different for every project/dataset and configures the analyses to be performed and databases to be used. The fields are described within the file.
- annotation: CSV file consisting of 5 mandatory columns
- name: unique(!) name of the query gene/region set
- features_path: one of the following
- path to a query region set as .bed file -> will be analyzed using LOLA, GREAT, pycisTarget and ORA_GSEApy, RcisTarget (using the region-gene association provided by GREAT)
- path to a query gene set as .txt file with one gene per line -> will be analyzed using ORA_GSEApy and RcisTarget
- path to a query (preranked) gene-score table with a header as .csv file, where the first column consists of gene-symbols/names and the second of corresponding gene-scores (e.g., from differential expression analysis results) -> will be analyzed using preranked_GSEApy
- background_name: name of the background gene/region set (only required for region- and gene-sets, leave empty for gene-score tables)
- background_path: path to the background/universe gene/region-set as .txt/.bed file (only required for region- and gene-sets, leave empty for gene-score tables)
- group: enrichment results are aggregated and visualized per analysis and database based on this group variable (e.g., gene/region-sets resulting from the same analysis)
Set workflow-specific resources
or command line arguments (CLI) in the workflow profile workflow/profiles/default.config.yaml
, which supersedes global Snakemake profiles.
Linting and formatting
Linting results
Using workflow specific profile workflow/profiles/default for setting default command line arguments.
FileNotFoundError in file /tmp/tmp4dm_gnm8/epigen-enrichment_analysis-e8a14b0/workflow/Snakefile, line 29:
[Errno 2] No such file or directory: '/path/to/enrichment_analysis_annotation.csv'
File "/tmp/tmp4dm_gnm8/epigen-enrichment_analysis-e8a14b0/workflow/Snakefile", line 29, in <module>
File "/home/runner/micromamba/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
File "/home/runner/micromamba/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 620, in _read
File "/home/runner/micromamba/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1620, in __init__
File "/home/runner/micromamba/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1880, in _make_engine
File "/home/runner/micromamba/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py", line 873, in get_handle
Formatting results
[DEBUG]
[DEBUG] In file "/tmp/tmp4dm_gnm8/epigen-enrichment_analysis-e8a14b0/workflow/rules/resources.smk": Formatted content is different from original
[DEBUG]
[DEBUG] In file "/tmp/tmp4dm_gnm8/epigen-enrichment_analysis-e8a14b0/workflow/rules/enrichment_analysis.smk": Formatted content is different from original
[DEBUG]
[DEBUG] In file "/tmp/tmp4dm_gnm8/epigen-enrichment_analysis-e8a14b0/workflow/rules/common.smk": Formatted content is different from original
[DEBUG]
[ERROR] In file "/tmp/tmp4dm_gnm8/epigen-enrichment_analysis-e8a14b0/workflow/rules/aggregate.smk": InvalidPython: Black error:
Cannot parse for target version Python 3.12: 21:10: resources:
(Note reported line number may be incorrect, as snakefmt could not determine the true line number)
[DEBUG] In file "/tmp/tmp4dm_gnm8/epigen-enrichment_analysis-e8a14b0/workflow/rules/aggregate.smk":
[DEBUG] In file "/tmp/tmp4dm_gnm8/epigen-enrichment_analysis-e8a14b0/workflow/Snakefile": Formatted content is different from original
[DEBUG]
[DEBUG] In file "/tmp/tmp4dm_gnm8/epigen-enrichment_analysis-e8a14b0/workflow/rules/envs_export.smk": Formatted content is different from original
[INFO] 1 file(s) raised parsing errors 🤕
[INFO] 5 file(s) would be changed 😬
... (truncated)