moiexpositoalonsolab/grenepipe
A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - for sampled individuals, and for pool sequencing.
Overview
Topics: variant-calls snakemake evolve-and-resequence population-genetics ancient-dna variant-calling pool-sequencing genomic-variant-calling snakemake-workflow
Latest release: v0.14.0, Last update: 2025-02-24
Linting: linting: failed, Formatting:formatting: passed
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/moiexpositoalonsolab/grenepipe . --tag v0.14.0
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
.
Grenepipe is a highly flexible workflow for variant calling from raw sample sequences,
with lots of bells and whistles. To configure this workflow, modify config/config.yaml
according to your needs, following the explanations provided in the file.
Furthermore, for the general usage of grenepipe, see our wiki. See there to get started with grenepipe.
Minimal input:
- Reference genome
fasta
file - Per-sample
fastq
files - Optionally, a
vcf
file of known variants to restrict the variant calling process
Process and available tools:
- Read trimming (single or paired end)
- Read mapping
- Optional read filtering, clipping, duplication removal, and quality score recalibration
- Damage profiling (optional; e.g., for ancient DNA)
- Variant calling and genotyping
- Variant filtering
- Frequency calling (for pool sequencing data, as an alternative to variant calling)
- Quality control, statistics, SNP annotation, reporting
- FastQC
- samtool stats
- samtool flagstat
- QualiMap
- Picard CollectMultipleMetrics
- bcftools stats
- snpEff
- VEP (Ensembl Variant Effect Predictor)
- MultiQC
Typical output:
- Variant calls
vcf
, raw and filtered, and potentially with annotations - MultiQC report (includes summaries of most other tools, and of the final
vcf
) - Snakemake report (optional)
Linting and formatting
Linting results
Using workflow specific profile workflow/profiles/default for setting default command line arguments.
WorkflowError in file /tmp/tmpiks6dpa1/moiexpositoalonsolab-grenepipe-1aae2c9/workflow/rules/initialize.smk, line 50:
Workflow defines configfile config.yaml but it is not present or accessible (full checked path: /tmp/tmpiks6dpa1/moiexpositoalonsolab-grenepipe-1aae2c9/config.yaml).
Formatting results
None