isugifNF/nanoPolish

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      isugifNF/nanoPolish  v1.0.0       
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Genome Informatics Facility |

---

Introduction

Polish a nanopore assembly using Racon and Medaka

isugifNF/blast is a nextflow pipeline

git clone [email protected]:nanoporetech/medaka.git

Installation and running on Ceres HPCC

Nextflow is already installed on Ceres HPCC. Therefore, running isugifNF/blast involves (1) allocating a debug node salloc -N 1 -p debug -t 01:00:00, (2) loading nextflow module load nextflow, and (3) running the pipeline nextflow run isugifNF/blast. The --help flag prints out the usage statement.

salloc -N 1 -p debug -t 01:00:00
module load nextflow
nextflow run isugifNF/blast --help

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 -resume

Usage Statement

```
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.

```

Common Errors

Unable to open file (file signature not found)

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
```