snakemake workflows ref:https://github.com/snakemake-workflows
ATAC-seq/ demo1: for replicate samples; ATAC-seq/ demo2: for plate method, 1 by 1 map, then merge. change from BWA to bowtie2;
R_script/ demo1: how to run parallel using snakemake in R environment, and wait for a file to generate.
(1) -n 模拟运行: 检查语法错误 $ snakemake -np -s /data/wangjl/soft/snakemakeWorkflow/R_script/demo1/main.sf -j 4
-p 打印正在运行的命令。 -j 4 使用线程数
(2) 画流程图: 总体是否符合逻辑 步骤流程图 $ snakemake -f -s s1.sf --rulegraph 2> /dev/null | dot -T pdf > workflow.pdf
样本流程图 $ snakemake --dag -s s1.sf | dot -Tpdf > dag.pdf 加 -forceall 则强制全部重新运行一次。
(3) 实际运行命令 $ snakemake -s /data/wangjl/soft/snakemakeWorkflow/R_script/demo1/main.sf -j 4