When parsing fastq file, convert to BAM

[cmatKhan]

Description of feature

It looks like in fastquorum from fgbio, they parse fastq with umi into a bam with tags. In the alignment step, they use samtools fastq to turn the bam back into a fastq file for alignment with bwa mem.

It is worth looking at this -- if the tags added to the fastq file are retained when converting from bam back to fastq back to bam, then it could potentially make the processing more straightforward

https://github.com/nf-core/fastquorum/blob/ea307015cf134358883d48fcd7a86b365a0a8bb2/modules/local/align_bam/main.nf