nf-core template @dev errors

[fmalmeida]

Description of the bug

When using the new developmental version of nf-core create command, which allows customisation of what to include in the created pipeline, I've seen that the starting pipeline, when skipping igenomes related snippets, the starting pipeline does not run because the getGenomeAttribute is still referenced in the WorkflowMain groovy lib.

This is what the YAML looks like:

name: nftemplate
description: NF Template built from nf-core template
author: Felipe Almeida
prefix: fma
skip:
  - ci
  - github_badges
  - igenomes
  - nf_core_configs

I think that it is related to making the lines

tools/nf_core/pipeline-template/main.nf

Lines 16 to 22 in 3ec4ca2

	/*
	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
	GENOME PARAMETER VALUES
	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
	*/
	params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')

optional as well related to igenomes.

Command used and terminal output

$ nf-core create -t custom_template.yml
$ nextflow run fma-nftemplate/main.nf --help


N E X T F L O W  ~  version 22.04.0
Launching `fma-nftemplate/main.nf` [angry_lalande] DSL2 - revision: 41f1eb01db
Unknown method invocation `getGenomeAttribute` on WorkflowMain type

 -- Check script 'fma-nftemplate/main.nf' at line: 18 or see '.nextflow.log' file for more details

System information

nf-core/tools version 2.5.dev0

[ErikDanielsson]

Good spot! It should be fixed in #1674.

[apeltzer]

Can confirm, at least for me it worked now!