epigen/genome_tracks
A Snakemake workflow and MrBiomics module for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, …) powered by the wrapper gtracks for the package pyGenomeTracks, and IGV-reports.
Overview
Topics: atac-seq bioinformatics pipeline python rna-seq snakemake visualization workflow biomedical-data-science genomic-regions genome-browser genome-track scrna-seq
Latest release: v2.0.0, Last update: 2024-11-16
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/genome_tracks . --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. 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. - sample annotation (sample_annotation): CSV file consisting of two mandatory columns
- bam: absolute path to mapped/aligned (and filtered) BAM file (*.bam).
- group:
- bulk samples: a string describing a group of samples to be merged (e.g., RNA_untreated), which are visualized together as one genome track. Note: multiple rows can have the same group and the respective BAM files will be merged using samtools.
- single-cell samples: path to a tab-separated metadata table wihtout header (TSV) where the first column are cell barcodes (CB) and the second a group variable (e.g., untreated/treated or cluster_1). Note: each single-cell BAM file is split into multiple BAM files according to the metadata file using sinto, and subsequenytly merged by group across all samples using samtools and downstream processed and visualized the same as bulk samples. It is important that the single-cell metadata.tsv is sample specific, because simply by chance different samples could have the same cell barcodes (CB).
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/tmp86w8spic/epigen-genome_tracks-b6df2ea/workflow/Snakefile, line 26:
[Errno 2] No such file or directory: '/path/to/myData_genome_tracks_annotation.csv'
File "/tmp/tmp86w8spic/epigen-genome_tracks-b6df2ea/workflow/Snakefile", line 26, in <module>
File "/home/michael/miniforge3/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
File "/home/michael/miniforge3/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 620, in _read
File "/home/michael/miniforge3/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1620, in __init__
File "/home/michael/miniforge3/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1880, in _make_engine
File "/home/michael/miniforge3/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/tmp86w8spic/epigen-genome_tracks-b6df2ea/workflow/rules/prepare.smk": Formatted content is different from original
[DEBUG]
<unknown>:1: SyntaxWarning: invalid escape sequence '\/'
[DEBUG] In file "/tmp/tmp86w8spic/epigen-genome_tracks-b6df2ea/workflow/rules/visualization.smk": Formatted content is different from original
[DEBUG]
[DEBUG] In file "/tmp/tmp86w8spic/epigen-genome_tracks-b6df2ea/workflow/rules/envs_export.smk": Formatted content is different from original
[DEBUG]
[DEBUG] In file "/tmp/tmp86w8spic/epigen-genome_tracks-b6df2ea/workflow/Snakefile": Formatted content is different from original
[DEBUG]
[DEBUG] In file "/tmp/tmp86w8spic/epigen-genome_tracks-b6df2ea/workflow/rules/common.smk": Formatted content is different from original
[INFO] 5 file(s) would be changed 😬
snakefmt version: 0.10.2