jeffhsu3 / cut_and_run

Snakemake Cut and Run Pipeline

cut_and_run

Snakemake Cut and Run Pipeline

Custom configuration for a snakemake pipeline loosely following the cutandrun2 pipeline

Currently Loaded Modules:

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

Step-by-step of install and analysis

1. Navigate to the new flowcell data output.

2. git clone this repository

   git clone https://github.com/jebard/cut_and_run

3. Activate the python anaconda environment (testing on CCR 04-05-21)

   conda activate snakemake

4. Edit the config.json file and cluster.json files

5. 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**

6. 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`

7. Pipeline should result in bigwig files