```
Usage:
The typical command for running the pipeline are as follows:

nextflow run isugifNF/nanoPolish --genome tail.fasta --reads test.fastq --chunkSize 25000 --model "medaka/medaka/data/r941_min_high_g303_model.hdf5" -profile singularity,condo


Mandatory arguments:

--genome                      genome assembly fasta file to run stats on. (./data/*.fasta)
-profile singularity           as of now, this workflow only works using singularity and requires this profile [be sure singularity is in your path]
--reads                       Raw nanopore reads to use in polish
Optional arguments:
--outdir                       Output directory to place final output
--threads                      Number of CPUs to use during the NanoPlot job [16]
--queueSize                    Maximum number of jobs to be queued [18]
--model                        Medaka hdf5 model used during polishing.
--chunkSize                    Number of fasta records to use when splitting the input fastq raw reads
--help                         This usage statement.

```

The hd5 files that are used as models are stored in gits large file storage `lfs`, if you do a git clone those files will just be text pointers unless you have git lfs installed.  If you run into a `Unable to open file (file signature not found)` error it is because the hd5 file is not an actual model file but a pointer to git's lfs storage.

In the medaka repo execute the following commands.

```
git lfs install
git lfs pull
```