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Table 1 - Command Line Tools to run your GWAS

Command Description Examples and additional infos
pwd Will print your present working directory  
ls Will print all files and directories within your present working directory If you put a path (absolute or relative) after ls it will print the content of this directory) e.g. ls /home will print the content of the folder home; If you add -l it will print the files and directories in a list that contains additional information such as permissions
mkdir Will make a new directory in your present working directory mkdir GWAS will make a directory called GWAS
cd Change directories If you only enter cd without an absolute or relative path, it will change to your home directory; Entering cd .. will change your current directory to the parent folder; Entering cd with an absolute or relative path will change the directory to the respective folder
nextflow run genepi/nf-gwas -c <nextflow.config> -r v0.5.0 –profile singularity Will run the gwas pipeline Adding -bg will continue to run the pipeline even if you close the command line; Adding -resume will continue the pipeline with the files that have already been generated by a run of the same config file (e.g. if you only change the settings for the annotation files, it does not have to rerun the whole pipeline); Exchange <nextflow.config> with the name of your config file; Version of the pipeline is adapted simply by changing the version (v0.5.0); Instead of singularity also dockerand slurm are currently available
htop Will display the current processes that are running Hit q to quit
vi A text editor in Linux that can display the content of a file, an alternative is for example nano (it can be used in the same way, but the advantage is that you can immediately start to modify the file) E.g. enter vi first-gwas.config to view the content of the first-gwas.config file;To quit just type in the following command and hit enter :q!; After running a GWAS you might notice a .nextflow.log file in you folder when you check via FileZilla but you don’t see them if you enter ls in the command line because the dot in the beginning of the file means its hidden. However, you can still look at the content of such a file by entering vi .nextflow.log