Snakemake Cut and Run Pipeline
module load gbc-samtools/1.12 gbc-deeptools/3.4.3 gbc-bowtie2/2.4.2 gbc-cutadapt/1.16 gbc-bedtools/2.29.1 python/py37-anaconda-2019.10 snakemake/5.7.1-py37
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git clone this repository
git clone https://github.com/jebard/cut_and_run
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Activate the python anaconda environment (testing on CCR 04-05-21)
conda activate snakemake
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Edit the config.json file and cluster.json files
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Ensure meta-data table contains all of the necessairy fields
** NOTE EXACT HEADERS HAVE TO BE ENFORCED or key errors will be thrown during processing**
- Launch jobs
The pipeline will utilize CCR resource to parallel execution. OTU table and statisics about merge rate, filter rate, hit rate wiil be placed under table
The use of --latency-wait allows for SLURM to catch up writing the files and posting the file handles so Snakemake can see them.
`snakemake --latency-wait 120 -p -j 100 --profile slurm`
- Pipeline should result in bigwig files