nf-core/vipr Usage

Please refer to the Nextflow documentation for generic Nextflow options, like -resume etc.

General Nextflow info

Nextflow handles job submissions on compute environments, and supervises running the jobs. Thus the Nextflow process must run until the pipeline is finished. We recommend that you put the process running in the background through screen / tmux or similar tool. Alternatively you can run nextflow within a cluster job submitted your job scheduler.

It is recommended to limit the Nextflow Java virtual machines memory. We recommend adding the following line to your environment (typically in ~/.bashrc or ~./bash_profile):

NXF_OPTS='-Xms1g -Xmx4g'

Running the pipeline

The typical command for running the pipeline is as follows:

nextflow run nf-core/vipr -params-file params.yaml -profile docker

This will launch the pipeline with the docker configuration profile using input paramters as defined in params.yaml. See below for more information about profiles.

Note that the pipeline will create the following files in your working directory:

work            # Directory containing the nextflow working files
results         # Finished results (configurable, see below)
.nextflow_log   # Log file from Nextflow
# Other nextflow hidden files, e.g. history of pipeline runs and old logs.

Updating the pipeline

When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you’re running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:

nextflow pull nf-core/vipr

Reproducibility

It’s a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you’ll be running the same version of the pipeline, even if there have been changes to the code since.

First, go to the nf-core/vipr releases page and find the latest version number - numeric only (e.g. 1.0). Then specify this when running the pipeline with -r (one hyphen), e.g. -r 1.0.

This version number will be logged in reports when you run the pipeline, so that you’ll know what you used when you look back in the future.

Main Arguments

-params-file

You can modify program behaviour and specify input files in a yaml configuration file. An example is given in example_params.yaml.

Please note: this is currently the only way to specify read input. The corresponding entries in params.yaml looks as follows:

params {
  samples:
    sample-name-1:
      readunits:
        readunit-1:
          fq1: path-to-R1.fastq.gz
          fq2: path-to-R2.fastq.gz
        ...
        readunit-n:
          fq1: path-to-R1.fastq.gz
          fq2: path-to-R2.fastq.gz
    ...
    sample-name-n:
      readunits:
        ..
}

So you can specify multiple samples and each samples can contain multiple fastq pairs (AKA readunits)

-profile

Use this parameter to choose a configuration profile. Each profile is designed for a different compute environment - follow the links below to see instructions for running on that system. Available profiles are:

• standard
  • The default profile, used if -profile is not specified at all. Runs locally and expects all software to be installed and available on the PATH.
  • This profile is mainly designed to be used as a starting point for other configurations and is inherited by most of the other profiles.
• none
  • No configuration at all. Useful if you want to build your own config from scratch and want to avoid loading in the default base config profile (not recommended).

See nextflow.config for more available profiles

--skip-kraken

Skips the optional Kraken metagenomics classifaction of your reads.

Reference Genomes

The pipeline requires you to specify close reference for samples (--ref-fasta, e.g. Zika) and a fasta reference for decontamination (--cont-fasta e.g. human) If you in addition also use Kraken (see above) you will need to specify the path to your Kraken database (--kraken-db).

You can add the above parameters to your params-file (see above). Then entries looks as follows

params {
  ref_fasta: "data/ref/DENV2-NC_001474.2.fa"
  cont_fasta: "/db/genomes/human_g1k_v37/human_g1k_v37.fasta"
  kraken_db: "/db/genomes/kraken/minikraken_20171019_8GB/"
  skip_kraken: false
  }
}

An example is given in example_params.yaml.

--outdir

The output directory where the results will be saved.

Job Resources

Automatic resubmission

Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with an error code of 143 (exceeded requested resources) it will automatically resubmit with higher requests (2 x original, then 3 x original). If it still fails after three times then the pipeline is stopped.

Custom resource requests

Wherever process-specific requirements are set in the pipeline, the default value can be changed by creating a custom config file. See the files in conf for examples.