A genome assemble and annotation pipeline based on nextflow and docker for bacteria
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-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
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-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
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-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.
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-Nextflow is based on java, so please comfirm that java in you PATH