Hello everyone, I developed a pipeline for my PhD and I'm trying to make it easily reusable by others, so I am trying to orient myself around nf-core standards. I have some questions about config files, like how to know which config options go into which config file, like output specifications and process specific resources and conda/container info (between

nextflow.config

,

conf/base.config

and

conf/modules.config

). Also, how do I best keep my personal config specifications (like where to save the work directory) separate from the default options. Do I just add another config file like

conf/isabel.config

and put my specifications there? At what level do I include this extra config file, just on the command line? Sorry for all the questions, I am still wrapping my head around this. If anybody could give me guidance or recommend a good resource I would really appreciate it. I tried to look through the nf-core help and the nextflow trainings but couldn't quite find something that clarified this for me. Thanks, Isabel

So for me any custom config like that should not belong in the pipeline itself that you share with others

Thank you that's really helpful

To answer some of your other questions: I think

nextflow.config

is largely about configuring the pipeline at a very basic level, i.e. set defaults / initialize all values.

base.config

is then a bit more specifically tailored towards a specific type of run (often pipelines offer choices on what you can do) and

base

kind of sets the "reasonable default", i.e. maybe you initialize some values to

null

or

""

in

nextflow.config

, but for the specific type of run that

base

configures they need to be set a to a different value.

modules.config

is configuring the modules that you use to work correctly in the context of your pipeline. e.g. specifying the output directory structure, and setting other things that are specific for how this module is used in the pipeline (e.g.

ext.args

)

isabel.config

, as maxime said, should not be in the pipeline directory, as this does not configure the "pipeline" but it configures a specific run, and other people probably do not want to run exactly what you do. From a data-management perspective

isabel.config

belongs to the data you are analyzing, and should be stored alongside the specific analysis.

Yes, I think I understand now, thank you. I might get back to you with follow-up questions as I work through this

Also, how do I best keep my personal config specifications (like where to save the work directory) separate from the default options.

This can actually be in your

~/.nextflow/config

(or wherever

$NXF_HOME

points to), see https://docs.seqera.io/nextflow/config#configuration-files