Building a custom nf-core analysis pipeline

Building a custom nf-core analysis pipeline#

These descriptions are based on the custom pipeline dsp_demo_nf_acore_vuegen which is used to highlight how an analysis notebook based on acore can be integrated with a report based on vuegen.

It is based on the nf-core tools and their template for a nextflow repository, see: nf-core/tools.

Using the template#

The instructions are brief on their website. Follow the command line instructions. Per default it is based on genomics data showing a fastqc analysis pipeline.

  • can be customized to have a prefix, e.g. dsp- instead of nf-core-. See customization options of nf-core pipelines create command. Set --organization dsp to have dsp- prefix.

  • pipeline structure explained here

  • an input schema (e.g. a SDRF file) can be defined using the schema-tutorial. The default pipeline has as single input a csv sample sheet, and an output directory.

Make adaptions to the pipeline created from the template#

  • edit the schema and remove the parameters which are not needed: nf-core pipelines schema build

  • then try to get it to run

Wave#

Can be used to auto-generate containers for workflow runs (if conda is not available).

  • from conda environment to containerized version

  • use wave profile from nf-core template config (will deactivate any pre-built docker or singularity containers)

Define the report path#

The file has to be linked in a process output explicitly, not just the folder, i.e. reports as output path would not display a report in reports/myreport.html, but reports/myreport* would.

Custom report can be added, e.g. from VueGen, to the reports tab. in Seqera Cloud using the tower.yml configuration file.

# tower.yml
reports:
  multiqc_report.html:
    display: "MultiQC HTML report"
  quarto_report.html:
    display: "VUEGen HTML report"

Hints#

  • the example was moved from a course repository to its separate repository dsp_demo_nf_acore_vuegen in order to make it executable on Seqera Cloud. The initial history can be found here.

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