benben-miao/OmicsFlowBuilder

Omics Flow Builders, such as Cromwell (Java), Nextflow (Java), Snakemake (Python).

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