nf-core template @dev errors (follow-up)

[fmalmeida]

Description of the bug

This issue is a follow-up of #1670.

The previous issue has fixed a part of the code that should be only written when template is created with igenomes . After fixing the previous spot, another part of the code that has the same pattern was spotted again.

custom_config.yml

#
# Using custom templates, nf-core tool wil create the repositories following this pattern:
# repository dir                : ${prefix}-${name}    # different name can be used with "-o"
# repository references in code : ${prefix/${name}
#

name       : nftemplate
description: NF Template built from nf-core template
author     : Felipe Almeida
prefix     : fma
skip:
  - ci                     # skips adding github ci files
  - github_badges          # skips adding nf-core github badges
  - igenomes               # skips adding igenomes configurations lines
  - nf_core_configs        # skips adding nf-core configs check-ups

After some first look-up, I believe the errors are appearing due to the following lines that are still present even after skipping igenomes:

tools/nf_core/pipeline-template/lib/WorkflowPipeline.groovy

Lines 15 to 18 in ed355ed

	if (!params.fasta) {
	log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
	System.exit(1)
	}

and

tools/nf_core/pipeline-template/workflows/pipeline.nf

Line 14 in ed355ed

def checkPathParamList = [ params.input, params.multiqc_config, params.fasta ]

Command used and terminal output

# When running the generated pipeline created without `igenomes`, the following errors appear.

$ nf-core create -t custom_config.yml --no-git -o . -f
$ nextflow run main.nf -profile docker,test --outdir .nextflow_results_tests

WARN: Access to undefined parameter `fasta` -- Initialise it to a default value eg. `params.fasta = some_value`
Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file.

System information

nf-core/tools version 2.5.dev0

[apeltzer]

Some more points in #1677

[mirpedrol]

Hi @fmalmeida, thanks for testing this functionality! :)

If I'm not wrong, when creating a template without igenomes the user will still need to provide a reference fasta file, this is needed for the test pipeline to run. For example:

example_reference.fa

>chr1
ACTGACTG
>chr2
AACCTTGG

nextflow run fma-nftemplate/main.nf -profile docker,test --outdir .nextflow_results_tests --fasta example_reference.fa

What we should do is specify this in the help message :)

[mirpedrol]

I modified the example command here #1691, let me know if you agree :)

[fmalmeida]

Hi @mirpedrol, I think this already helps. But, additionally, I really think that the -profile test should be self-sufficient. For example, have a params.fasta already pre-defined in them so users can directly teste and overview a pipeline, in this case, the example template.

[mirpedrol]

You are right @fmalmeida, I added a fasta file to the test config files :)

[fmalmeida]

Thanks 😄