nf-metaomics-daisychain Documentation

Here is the user documentation for nf-metaomics-daisychain. It is a meta-pipeline that includes several pipelines from nf-core.

Quickstart

Write a meta-pipeline-params.yml that enables which pipelines you want to daisy-chain together.

# Run pipelines
fetchngs_enabled: true
detaxizer_enabled: false
createtaxdb_enabled: false
ampliseq_enabled: false
taxprofiler_enabled: true
eager_enabled: false
magmap_enabled: false
mag_enabled: false
metatdenovo_enabled: false
differentialabundance_enabled: false
metapep_enabled: false
phageannotator_enabled: false
funcscan_enabled: false
phyloplace_enabled: false
gms_metaval_enabled: false

For each pipeline you want to run, you’ll need to create a params.{yml,json} file (Ideally name it after the pipeline e.g., fetchngs-params.yml). You can do this with nf-core pipelines launch <pipeline>, or use the launch page on the nf-core website. For non-nf-core pipelines, you’ll have to create this manually. In most cases you’ll be forced to enter a value for --input, but that should be removed before using the meta-pipeline.

Add these files to your meta-pipeline-params.yml:

## Pipeline inputs
fetchngs_params: 'tests/params/fetchngs-params.json'
...

Command line interface instructions can also be added to the meta-pipeline-params.yml:

## Command-line options
all_cli: '-resume -ansi-log false'
fetchngs_cli: '-r 1.12.0 -profile docker'
taxprofiler_cli: '-r 1.2.3 -profile docker,test'

Custom configs can also be added similarly:

## Additional configuration files
fetchngs_config: 'configs/multiqc.config'
taxprofiler_config: 'configs/multiqc.config'

The meta-pipeline is then run using:

nextflow run mahesh-panchal/nf-metaomics-daisychain -params-file meta-pipeline-params.yml