Command Line Options¶
This section explores the different options that are possible when running the tool. Before running the tool, you can first run the command mitopipeline -d in order to download all of the dependencies necessary for the steps in your pipeline if you do not specify a tools directory.
Downloading Software¶
| Option | Description |
|---|---|
-d or --download |
REQUIRED.
Option to download softwares for steps not listed in -r.
|
-r or --remove |
Specifies steps that won’t be run in the pipeline.
Input: <name of steps>
Default: None
|
Running Pipeline¶
| Option | Description |
|---|---|
-s or --start |
REQUIRED.
Specifies the directory that contains the files to be run on.
Input: <path/to/startdirectory>
|
-g, --genomes |
REQUIRED.
Specifies location of the folder that contains the human reference genomes.
The required genomes for this pipeline are:
- hg38-nochr.fa (the human genome without the mitochondrial genome)
- hg38.fa (the entire human genome)
- rCRS.fa (the human mitochondrial genome).
The file names must match the ones listed here so that the steps are able to find the files. You can also download these human references genomes from the UCSC genome browser.
Input: <path/to/REFs/directory>
|
-t, ---tools |
REQUIRED.
Specifies the location of the folder that contains all of the 3rd party software. The executables must be in a folder with the same name as the software, i.e. gatk should have its default executable within </path/to/tools/gatk> .
Input: <path/to/tools/directory>
Default: <path/to/mitopipeline/tools/directory>
|
-o or --output |
Specifies where to store the output of the pipeline results. Will create folders for each step within the output directory.
Input: <path/to/output/directory>
Default: current directory
|
-l or --slurm |
Use the slurm workload manager to submit batch jobs for each step of the pipeline
Default: False
|
-w or --workers |
Specifies the number of workers to use when running the pipeline.
Input: integer
Default: 1
|
-r or --remove |
Specifies steps that won’t be run in the pipeline. The names of the steps are:
[‘extractmito’, ‘splitgap’, ‘clipping’, ‘removenumts’, ‘gatk’, ‘snpeff’, ‘annovar’]
Input: <name of steps>
Default: None
|