1- Use conda to create an environment using Covid19.yaml
ex: conda env create --name NAME --file Covid19.yaml
conda activate NAME
2- Go to the directory you want to run the pipeline in ex: cd /user/home/myfastq
3- Copy the files that were supported by Vipin to the previous directory from step 2 (Snakefile and config.yaml)
4- Run the following:
snakemake -s ./Snakefile ~/E81581/result/1.txt --latency-wait 120 -j all -p
E81581:- Directory contains 2 fastq files; like H3GLWDRXY-1-IDUSU178_S63_L001_R1_001.fastq.gz H3GLWDRXY-1-IDUSU178_S63_L001_R2_001.fastq.gz Naming is important, it should be anything_R1_001.fastq.gz and anything_R1_001.fastq.gz result:- is the name of the output directory (feel free to use other names) 1.txt:- anchor file (feel free to use other names)
5- To change any parameter refer to config.yaml