Rename FASTQ files and check sample ids

[skrakau]

• rename all short read FASTQ files to ensure consistent names in reports from FastQC and allow non-unique read file base names
• added check for unique sample IDs, return error otherwise

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated
• If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repo

[d4straub]

To me this is not readable. What does this do?

Guessing: If file "${name}_R1.fastq.gz" doesnt exist than link reads[0} to "${name}_R1.fastq.gz"
If yes, could you write that in an easier understandable way? With an in if such? Like this its short but hard to read, in my opinion.
How does this interact with includeInputs: true, havent seen that one before, I guess it is important if the above link isnt created. But what happens is the link is actually created? Isnt than reads[0] also added to the output channel, provided it follows *.fastq.gz as well?

[skrakau]

Oh true, I forgot to add the corresponding glob pattern, thanks for reviewing!

includeInputs is important, because by default input files will not be used for the output (https://www.nextflow.io/docs/latest/process.html#output-path), even if the name matches.
I didn't want to rename the input files, that's why I did it this way.

[d4straub]

LGTM!