FastqToBam with a external UMIs fastq

[migrau]

Description of feature

Is it possible to include a 3rd fastq file including only the UMIs, for the FastqToBam step? What I normally do is:

fgbio --compression 1 --async-io FastqToBam --input {input.fqR1} {input.fqR2} {input.umifq} --read-structures +T +T +M --sample {params.samplename} --library {params.samplename} --output {output}

Many thanks, @nh13! Very exciting seeing a nf-core pipeline for fgbio.

[adamrtalbot]

See #11 !

[adamrtalbot]

One thing we need to do is add an example UMI FASTQ file to https://github.com/nf-core/test-datasets for testing purposes.

[nh13]

It would be great to support any subset of the standard four reads that can be generated in a paired end library:

1. index1/i7
2. index2/i5
3. read1/R1
4. read2/R2

The UMI could be in any of these reads, and FastqToBam would be able to handle it.

[nh13]

See #38

[nh13]

Done!