Add found_in tag and nf-test to call repeat expansions

[fellen31]

Closes #391

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!
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[Lucpen]

If its a sample_bam with its corresponding sample_bai, wouldn't it be better to output them together as one channel?

[fellen31]

I think what I wrote in the previous comment holds true somewhat here as well, some tools that require a bam file do not require a bai (although to be fair most do).

I think the tests get easier to read and write if we can standardise and know that there's only a meta and a file in the output channels from each workflow.

E.g.:

path(workflow.out.project_vcf[0][1])).vcf.variantsMD5,
{ assert process.out.tbi[0][1].endsWith(".tbi") }

vs.

path(workflow.out.project_vcf_tbi[0][0][0])).vcf.variantsMD5,
{ assert process.out.project_vcf_tbi[0][0][1].endsWith(".tbi") }

Especially if there's a mix of output channels with different number of elements (which there will be, because not all file types have an index).

Most nf-core modules output one file per output, so to me it makes sense to try to keep subworkflows the same as well.

[Lucpen]

I think that in this case it's a bit different because you could end up putting together the wrong bam with the wrong bai but it's a mater of taste. So I will approve the PR :)

[Lucpen]

LGTM!

[Lucpen]

I think that in this case it's a bit different because you could end up putting together the wrong bam with the wrong bai but it's a mater of taste. So I will approve the PR :)