nextflow-io/nextflow

Support custom config and params-file in `nextflow config` command

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#4,275 opened on Sep 6, 2023

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 (3 comments) (0 reactions) (0 assignees)Groovy (784 forks)batch import
good first issue

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Description

New feature

The nextflow config command is useful for printing the configuration of a project, but could be improved if it also allowed providing custom config files with -c/-C/-params-file just like nextflow run.

Usage scenario

We can run nextflow config main.nf -profile custom_profile to see the configuration that would be used with a subsequent nextflow run command. However, users often wish to supplement or override the config and params with -c, -C, or -params-file when executing a workflow. Allowing nextflow config to accept these arguments would assist users and developers in understanding how the configuration is parsed and prioritized for debugging purposes.

Suggest implementation

Ideally it would re-use the same logic as nextflow run to parse the configuration & parameters, and use the same CLI syntax, e.g.

nextflow config main.nf -params-file custom.yml -C custom.config

Contributor guide

Research direction
Examine how `nextflow run` parses ` c`, ` C`, and ` params file` arguments, then add similar parsing to the `nextflow config` command. Ensure the same configuration priority logic is reused.
Tech stack
groovy
Domain
backend
Issue type
Feature
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-3 hours
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
GitGroovy/JavaNextflow
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
75