Remove lib directory and replace it with granular utils_* subworkflows

[drpatelh]

Some things left to do that I took note of and might be worth splitting up into separate issues:

• Use MultiQC for software versions and remove custom/dumpsoftwareversions
• Remove input_check.nf, check_samplesheet.py and samplesheet_check.nf and replace with nf-validation
• Attach MultiQC report in completion email. This has been removed in the current implementation in this PR.
• Add in methods description implementation. This has been removed in the current implementation in this PR.

Edit by @mashehu:
Not in the scope of this PR:

• Move ALL subworkflows and workflows into their own named folder. See here
• Remove modules.config and have individual nextflow.config file in component folders instead. See here
• Do not remove nextflow.config when updating modules/subworkflows
• Update Github Actions for cloud tests on AWS and Azure. See here and here

[drpatelh]

@mirpedrol I added a checkProfileProvided function in 5214976

We will need to update the relevant subworkflow in nf-core/modules.

[drpatelh]

@mashehu @mirpedrol not sure whether you plan to or are doing this already but I thought we could use nf-test to check the pipeline tests pass as part of the nf-core/tools tests. Then we just add different combinations of nf-core create with different components and run every nf-test found from the root folder downwards which will induce module/subworkflow/workflow/pipeline tests too.

Would like to have a quick chat with you both next week if you have some time. Ping me on Slack and we can sort out a time.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (fca9d74) 73.53% compared to head (28c0196) 73.46%.
Report is 60 commits behind head on dev.

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[mashehu]

Still need to run a few test runs locally, but I think it looks good