Initial commit to add fq lint module

[oligomyeggo]

Addition to the RNA-seq pipeline to include the fq lint module and validate single-end or paired-end FastQ files. This will prevent the pipeline from continuing and running more computationally-heavy steps on corrupted FastQ files, and will address open issue #1281 .

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/rnaseq branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[pinin4fjords]

In general, this will be a great contribution!

But any 'nf-core' components (modules, subworkflows) need to be updated in the modules repo first (e.g. here). Then we can use the nf-core tooling to update those components in the subworkflow.

It would also be good to capture the outputs. So the subworkflow should have an output channel for the linting report, and we should set a publishing rule to place the output in the output directory. I can help with that when we get there.

[pinin4fjords]

I see this change has not been made on nf-core/modules- it needs to be done there, and then the component added here

[pinin4fjords]

Suggested change

	ch_reads
	.map {
	meta, fastqs ->
	return [meta, fastqs.flatten()]
	}
	.set { ch_fastq_lint }
	//
	// MODULE: Lint FastQ files
	//
	if (!skip_linting) {
	FQ_LINT (
	ch_fastq_lint
	)
	ch_versions = ch_versions.mix(FQ_LINT.out.versions.first())
	}
	//
	// MODULE: Lint FastQ files
	//
	if (!skip_linting) {
	FQ_LINT (
	ch_fastq_lint.map{ meta, fastqs -> [meta, fastqs.flatten()] }
	)
	ch_versions = ch_versions.mix(FQ_LINT.out.versions.first())
	}

(but again, this needs PR'ing to the modules repo first)

[pinin4fjords]

Also, the linting outputs should be added as a subworkflow output

[oligomyeggo]

Thanks so much for reviewing @pinin4fjords ! I opened a PR in the modules repo here: nf-core/modules#7000