Jennifer

Test Run of nanoQCtrim

Installation

git clone https://github.com/isugifNF/nanoQCtrim.git
cd nanoQCtrim

nextflow run main.nf --help

See help statement

N E X T F L O W  ~  version 20.07.1
Launching `main.nf` [cheesy_pasteur] - revision: 5b10f49a60
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                                    \\---------//       
      ___  ___        _   ___  ___    \\-----//        
       |  (___  |  | / _   |   |_       \-//         
      _|_  ___) |__| \_/  _|_  |        // \        
                                      //-----\\       
                                    //---------\\       
      isugifNF/nanoQCtrim  v1.0.0       
    ----------------------------------------------------
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.

Singularity

Dependencies are made available via singularity containers. Nextflow should automatically download the singularity containers, unless there are internet connection issues.

nanoplot_container = 'quay.io/biocontainers/nanoplot:1.32.0--py_0'
downpore_container = 'quay.io/biocontainers/downpore:0.3.3--h375a9b1_0'

Test Dataset

Find dataset.

# fetch dataset here

Running the Pipeline

Basic run here after there's a test dataset.

nextflow run main.nf \
  --fastqs "data/*.fq" \
  --account isu_gif_proj \
  -profile singularity,atlas \
  -resume

Test Runs

• Ceres
• Atlas
• Condo
• Nova
• Local Mac
• Local PC

Should we be looking into travis.ci?