GenomicsFlowBuilder repository maintain the flow code builders, such as Cromwell (Java), Nextflow (Java) and Snakemake (Python). The ATAC_Seq_Flow folder is a template project organized by snakemake framework.
conda create -c bioconda -c conda-forge -n snakemake snakemake
conda activate snakemake
# conda deactivate snakemake# Run Test
snakemake --snakefile atac_seq_flow.py --dryrun
# Run Dag
snakemake --snakefile atac_seq_flow.py --dag
# Run Graph
# mamba install graphviz
snakemake --snakefile atac_seq_flow.py --dag | dot -Tpdf -o graph.pdf
snakemake --snakefile atac_seq_flow.py --dag | dot -Tpng -o graph.png
# Run Jobs
snakemake --snakefile atac_seq_flow.py --printshellcmds --jobs 3 &
# Run Details
snakemake --help