Run the pipeline:

step 1: prepare ref index using bowtie2-build .fasta
1. define samples and reads wildcard, make sure the combination could locate the file; 
2. define ref genome in macs2 peakcall -g; 
3. check the thread setting whether it fits the # environment; 
4. set the ref index base name correctly in the alignment part)
5. pull the docker image: docker pull jiangyanyu/yeast_chipseq:1.0

step 2: run docker and link env folder, fastq folder, tmp folder, ref index folder and output folder.
1. create an output folder which will contain all output files
2. copy the Snakefile (downloaded from https://github.com/JiangyanYu/yeast_chipseq) to output folder 
4. download env folder (downloaded from https://github.com/JiangyanYu/yeast_chipseq)
5. enter container
docker run -it --rm --name Chip_preprocessing \
 -v /home/yu.j/sciebo/G4/Zuo1ChIPseq2020/output/:/output/ \
 -v /home/yu.j/sciebo/G4/Zuo1ChIPseq2020/fastq/:/data/ \
 -v /home/yu.j/sciebo/G4/Zuo1ChIPseq2020/envs/:/envs/ \
 -v /home/yu.j/sciebo/G4/S288C_reference_genome_R64-4-1_20230830/bowtie_index/:/data/bowtie2-index/genomefiles \
 jiangyanyu/yeast_chipseq:1.0 /bin/bash

step 3: run file
snakemake --snakefile /output/Snakefile --use-conda --cores 28 --verbose