use nf-core framework for CLI help and log messages

fmalmeida / MpGAP

Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads

https://mpgap.readthedocs.io/en/latest/

GNU General Public License v3.0

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Closed fmalmeida closed 2 years ago

fmalmeida commented 2 years ago

Change the pipeline configurations a little bit to:

[x] Better reorganize the config files, updating standard to do not load any other profile as is common for NF pipelines
[x] Better separate defaults params from the main config and script
[x] Use label resources to better manage parallel jobs as it is done by nf-core
[x] Use more of nf-core framework and Groovy libs to provide beautiful and cleaner CLI help and log messages

fmalmeida commented 2 years ago

Implementation going on in dev branch

fmalmeida commented 2 years ago

Seems properly implemented. Must now check documentation to identify snippets that need to be updated.

fmalmeida commented 2 years ago

It has been added.