Tuberculosis Genomic Pipeline
git clone https://github.com/dbespiatykh/TBGenoPipe.git && cd TBGenoPipe
micromamba create -n snakemake -c conda-forge -c bioconda snakemake mamba
micromamba activate snakemake
chmod +x TBGenoPipe
# test
./TBGenoPipe -t 6 --type fastq -i config/reads_PE_SE.tsv --test
# run
./TBGenoPipe -t 6 --type fastq -i config/reads_PE_SE.tsv -o results_output
git clone https://github.com/dbespiatykh/TBGenoPipe.git && cd TBGenoPipe
chmod +x TBGenoPipe
docker pull --platform linux/amd64 snakemake/snakemake:stable
#test
sudo docker run \
-it \
--rm \
-v "$(pwd)":/mnt/TBGenoPipe \
--platform linux/amd64 snakemake/snakemake:stable \
bash -c "cd /mnt/TBGenoPipe && ./TBGenoPipe -t 6 --type fastq -i config/reads_PE_SE.tsv --test"
#run
sudo docker run \
-it \
-rm \
-v "$(pwd)":/mnt/TBGenoPipe \
--platform linux/amd64 snakemake/snakemake:stable \
bash -c "cd /mnt/TBGenoPipe && ./TBGenoPipe -t 6 --type fastq -i config/reads_PE_SE.tsv -o results_output"
TBGenoPipe (A pipilene for Mycobacterium tuberculoisis genomic analysis)
Usage: TBGenoPipe [options]
Options:
--type [sra/fastq] Type of the input data
-i, --input Input samples table
-o, --output Output directory
-t, --threads Number of threads to use
--test Run pipeline in a dry-run mode
Important
Instructions for input table formats can be found here.