nanoQCtrim

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      isugifNF/nanoQCtrim  v1.0.0       
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Genome Informatics Facility |

---

Introduction

isugifNF/nanoQCtrim is a nextflow pipeline to assess the nanopore read quality using Nanoplot and trim adaptors using downpore.

Installation and running

See usage statement

```
Usage:
The typical command for running the pipeline is as follows:
nextflow run isugifNF/nanoQCtrim --fastqs "/Path/to/rawdata/folder/*.fastq" -profile condo

Mandatory arguments:

--fastqs                      fastq files to run nanoplot on. (/data/*.fastq)

Optional arguments:
--outdir                      Output directory to place final BLAST output
--threads                      Number of CPUs to use during the NanoPlot job [16]
--queueSize                    Maximum number of jobs to be queued [18]
--account                      Some HPCs require you supply an account name for tracking usage.  You can supply that here.
--help                         This usage statement.
```

Expected Output

• out_dir/nanoplot/fileName_combined
  • fileName_NanoStats.md -- NanoPlotQC summary in markdown format
  • many png files for each of the plots generated.
• out_dir/downpore/
  • fileName__adaptersRemoved.fastq -- Trimmed read output from downpore.

Dependencies if running locally

Nextflow is written in groovy which requires java version 1.8 or greater (check version using java -version). But otherwise can be installed if you have a working linux command-line.

java -version
curl -s https://get.nextflow.io | bash

# Check to see if nextflow is created
ls -ltr nextflow
#> total 32
#> -rwx--x--x  1 username  staff    15K Aug 12 12:47 nextflow

Credits

This workflow was built by Andrew Severin (@isugif)

Potential Errors

• ssh://[email protected]/isugifNF/assemblyStats.git: Auth fail

  This occurs if you have not set up github authorization on your remote machine yet. See this Introduction to Github Tutorial on how to set up an ssh key.

• WARN: Singularity cache directory has not been defined

  If you are planning on running this program more than once or more than one workflow it is best to set the NXF_SINGULARITY_CACHEDIR to a common location

  export NXF_SINGULARITY_CACHEDIR=/location/of/singularity/container/folder
  

  Place that in your .bashrc file.