1.GenomicsFlowBuilder

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.

2.Test ATAC_Seq_Flow

2.1 Conda environment

conda create -c bioconda -c conda-forge -n snakemake snakemake
conda activate snakemake
# conda deactivate snakemake

2.2 Snakemake commands

# 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

2.3 Flow graph