Nextflow Best Practices

Best Practices

Following are some best practices for creating tools. Our intention is that this document will evolve as descriptor languages evolve so feel free to provide suggestions and/or improvements.

In this tutorial, we will be using examples from one-workflow-many-ways.

Authorship Metadata

Dockstore parses metadata and allows it to be used in Dockstore search which helps others find your tool/workflow more easily. “Author” is one of the metadata fields that is searchable:

Additionally, metadata is displayed in the tool/workflow’s “Info” tab. The highlighted sections below will appear once metadata is added to the descriptor:

For all developers, we highly recommend the following minimal metadata for your tools and workflows.

This example includes author and description metadata:

nextflow-workflow/nextflow.config

manifest {
    description = 'Generate some stats on a BAM file'
    author = 'Andrew Duncan'
}

params {
    flagstat_to_json = 'flagstat2json.sh'
    bamqc_pl = 'bamqc/bamqc.pl'
    bamfile = 'bamqc/t/test/neat_5x_EX_hg19_chr21.bam'
    bedfile = 'bamqc/t/test/SureSelect_All_Exon_V4_Covered_Sorted_chr21.bed'
    outjson = 'bamqc/t/test/neat_5x_EX_hg19_chr21.json'
    samtools = 'samtools'
}

This results in the workflow’s Info Tab being populated like:

Next Steps

At this juncture, you have completed all of the developer tutorials.

Please continue onwards with specific topics of interest via our Advanced Developer Topics or our End User Topics