Simplify charliecloud profile

[phue]

With charliecloud v0.22, docker ENV layers are supported. Nextflow supports this feature since v21.03.0-edge (nextflow-io/nextflow@4553648).
This means we don't have to explicitly set the PATH variable within the container anymore, greatly simplifying the config.

I included a nag that this requires v21.03.0-edge

tools/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config

Lines 81 to 84 in 7261ebd

	charliecloud {
	manifest.nextflowVersion = '>=21.03.0-edge'
	charliecloud.enabled = true
	}

but I don't think this will work because the manifest is set after the profile config:

tools/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config

Lines 121 to 129 in 7261ebd

	manifest {
	name = '{{ cookiecutter.name }}'
	author = '{{ cookiecutter.author }}'
	homePage = 'https://github.com/{{ cookiecutter.name }}'
	description = '{{ cookiecutter.description }}'
	mainScript = 'main.nf'
	nextflowVersion = '>=20.04.0'
	version = '{{ cookiecutter.version }}'
	}

So either we move that up or remove the override in the charliecloud profile entirely, assuming that there will be no tools release before 21.04.0?

[codecov]

Codecov Report

Merging #867 (ddcafcd) into dev (bdba529) will increase coverage by 1.31%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##              dev     #867      +/-   ##
==========================================
+ Coverage   73.20%   74.52%   +1.31%     
==========================================
  Files          22       29       +7     
  Lines        2784     3183     +399     
==========================================
+ Hits         2038     2372     +334     
- Misses        746      811      +65     

Impacted Files	Coverage Δ
nf_core/bump_version.py	85.93% <ø> (-0.22%)	⬇️
nf_core/lint/schema_params.py	78.94% <0.00%> (-5.27%)	⬇️
nf_core/lint/actions_awstest.py	83.33% <0.00%> (ø)
nf_core/lint/files_exist.py	81.39% <0.00%> (ø)
nf_core/lint/actions_ci.py	94.33% <0.00%> (ø)
nf_core/lint/actions_schema_validation.py	90.62% <0.00%> (ø)
nf_core/lint/actions_awsfulltest.py	93.10% <0.00%> (ø)
nf_core/__init__.py	100.00% <0.00%> (ø)
nf_core/lint/__init__.py	79.72% <0.00%> (ø)

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[ewels]

The downside of modifying this in the profile is that when it gets out of date, this will clobber anything specified by the pipeline author in the nextflow.config.. I'm inclined to leave it out and let people figure this out themselves for now. I guess there aren't loads of people using Charliecloud yet so shouldn't affect a lot of people? And will be mainstream version by the time it's widely used I would think..

[phue]

Agreed, it is not going to affect a lot of users so we're probably good in leaving it out.
But generally, with nextflow switching to a 6 month release cycle, it might be good to think about how we could handle different version requirements for different profiles (as an example, the current edge requirement for nf-core/rnaseq only affects the singularity profile)

[ewels]

Could maybe open a new issue to think about the question of multiple minimum required versions 👍🏻

Can't think of anything obvious now except manually adding checks for this in a boilerplate library file. That shouldn't be too difficult in the new DSL2 template structure I think.