Suggestion: support genotyping from BAMs

[Will-Tyler]

Description

Currently, the Nextflow workflow uses the reads parameter during the graph_align_reads process. However, users may opt to run the pipeline using alignments (BAM files) instead of reads. So I think the workflow should check the bams parameter for this. I checked that GraphAligner supports BAM inputs—not sure about the others.

[cgroza]

Hi
Thank you for the suggestion.

It would not be too hard to have --reads detect BAM inputs and convert it on the fly to the appropriate format for the alignment tool.
I will implement this in the near future.

[Will-Tyler]

Sounds reasonable to me. Ideally, if GraphAligner is used as the graph genotyping method, the GraffiTE pipeline should not have to convert the BAM file to another format since GraphAligner supports BAM file inputs. However, GraffiTE may need to convert the BAMs to another format for the other graph methods (Pangenie and Giraffe)—I haven't looked to see if the other tools can accept BAM inputs.