Configuration¶

Config-file¶

Create a custom config file
Most of the required flags won't change across quicksand processings, like the --db or the --genomes flag.
To re-use parameters and other configs across runs, create a config-file e.g. quicksand.config as described below and hand it over to the pipeline with the -c flag:

//
// just put all the parameters that are used by default here

params {
    db         = "path/to/kraken/Mito_db_kmer22"
    genomes    = "path/to/genomes"
    bedfiles   = "path/to/masked/"
}

//add singularity by default to the pipeline
//bind: add shared drives (if necessary)
//cacheDir: where to download the container

singularity{
    enabled = true
    autoMounts = true
    runOptions = "--bind /mnt/"
    cacheDir   = "path/to/singularity/"
}

Please see the available configuration options in the nextflow documentation

And run quicksand:

nextflow run mpieva/quicksand -c nextflow.config [...] -profile singularity

Environmental variables¶

The following nextflow specific ENV variables can be set:

NXF_SINGULARITY_CACHEDIR <path> Where to save the pulled Singularity-images
NXF_WORK                 <path> Corresponds to the -w flag
NXF_OPTS                 <ARGS> Hand args over to the Java Virtual Machine.
                         In case of a heap-space error, assign more space with the
                         Arguments: "-Xms10g -Xmx20g" (allocates 128GB heap-space for the run)

Intermediate files¶

Nextflow stores intermediate files and directories in the work directory. You can delete the folder after the run:

rm -fr work/