A genome assemble and annotation pipeline based on nextflow and docker for bacteria

1. -STEP01: -INSTALL NEXTFLOW FOR PIPELINE:

   if [ -d ~/bin ];then
   	mkdir -p ~/bin
   fi
   cd ~/bin
   curl -s https://get.nextflow.io | bash  OR INSTALL WITH CONDA : conda install nextflow 

   -ECHO NEXTFLOW TO PATH:

   echo 'export PATH=$PATH:~/bin' >> ~/.bashrc
   source  ~/.bashrc

   -This pipeline is based one nextflow DSL2 , so you can run nextflow self-update to update NEXTFLOW to new version

2. -STEP02: -DOCKER DEPLOY:

   curl -sSL https://get.daocloud.io/docker | sh

   -DOCKER permission:

   sudo groupadd -g 999 docker
   sudo gpasswd -a ${USER} docker
   sudo systemctl restart docker
   sudo chmod a+rw /var/run/docker.sock

   -DOCKER TEST

   docker ps -a

3. -STEP03: -RUN PIPELINE:

   nextflow run main.nf --reads 'reads/*.fq.gz'	

   -Tips: When you first install docker and run the process, it will automatically download the required docker image and activate it.

4. -Nextflow is based on java, so please comfirm that java in you PATH