Configuration¶

Config-file¶

create a custom config file
Since most of the required flags won't change across runs - like the --db or the --genomes flag, it is possible to create a custom nextflow.config file
to define these parameters as default values for the pipeline.
Create a config-file nextflow.config as outlined below and hand it over to the pipeline with the -c flag:

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

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

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

Please see the available configuration options in the nextflow documentation

And run the pipeline:

nextflow run mpieva/quicksand -c nextflow.config --split path/to/split -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: "-Xms128g -Xmx128g" (allocates 128GB heap-space for the run)

Intermediate files¶

To run all processes separate from each other Nextflow creates intermediate files and directories that are stored in the work directory. You can delete the folder after the run:

rm -fr work/