eager
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nf-core
Mapped reads as input to metagenomic screening
nf-core/eager feature request
Allow mapped reads to be converted to fastq for input into metagenomic screening steps.
Is your feature request related to a problem? Please describe
Lack of flexibility in choosing what reads go to metagenomic screening steps
Describe the solution you'd like
Ability to select either mapped reads (with a given mapping quality threshold) OR unmapped reads as conversion to fastq for input into metagenomic screening step. (eg run mapping against a fasta of all microbial diversity, discard all non-mapped reads, run all mapped reads into metagenomic screening)
Describe alternatives you've considered
No current work arounds for getting mapped reads --> fastq for processing. Alternative is to have reference genome include more species that you want to filter out.
Additional context
A DAG diagram of where reads are ending up as inputs to other tools would be a huge help for interpretability of the pipeline, and as a potential ""dry"" run of the pipeline to make sure users know what will happen to their data.
A DAG diagram of where reads are ending up as inputs to other tools would be a huge help for interpretability of the pipeline, and as a potential ""dry"" run of the pipeline to make sure users know what will happen to their data.
Not sure what you mean here? Dry run stuff would be at a nextflow level however and not in scope here.
