Template: Better handling of params.fasta requirement

[ewels]

Description of feature

We currently have a check for params.fasta hardcoded into lib/WorkflowPipeline.groovy:

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

Lines 18 to 20 in 0912990

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

This is not very easy to find and tricky for people creating non-genomics pipelines.

Needs one or more of the following:

1. A // TODO nf-core: comment to flag it for review with nf-core lint
2. Some inclusion in the templating feature switches, to exclude it for non-genomics workflows
3. Moving out of lib to somewhere more visible? 🤔 eg. we already have similar checks here:
   

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

   Lines 17 to 18 in 0912990

   	// Check mandatory parameters
   	if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }

My preference would be (3) unless there's a specific reason for having it where it is currently.. @drpatelh ?

[drpatelh]

I put it in lib/ so it sits with all of the other params checks we do so they are all together in a single initialise function and to avoid adding loads of boilerplate to the main workflows.

Think I added input in the main workflow because it is one of the only inputs that can be staged directly as a channel and doesn't need to pass through a module/sub-workflow like the reference files.

I would prefer (1) because you can quite easily search for the error code in VS code and find where it is.

(2) would be good either way.

[mirpedrol]

params.fasta is now outside of the lib directory and can be skipped when creating a pipeline