add --save_merged_fastq for merging technical repeats to fetchngs

[ojziff]

Description of feature

Hi nfcore/fetchngs team,

It would be awesome to add --save_merged_fastq for merging technical repeats to fetchngs. Would be very useful for downstream programs that cant deal with technical repeats.

Often easy to identify technical repeats from GEO because although technical repeats each have unique run_accession they share the same experiment_alias.

Many thanks,
Oliver

[Midnighter]

@jfy133 I think we have working code for this in funcscan or taxprofiler already, right?

[jfy133]

I guess this one?

https://github.com/nf-core/taxprofiler/blob/43ea8d299cb96890ee12e1d32349dd7a7a5726d0/workflows/taxprofiler.nf#L165-L201

[drpatelh]

True origins from rnaseq here!

Just need to figure out how we report the ids in this case after merging i.e. if this parameter is provided do we name files relative to experiment id.

[jfy133]

Maaaan do we need subworkflows to stop reinventing the wheel ;)

[Midnighter]

Now that we have subworkflows, is this already tackled, should we tackle this?