Alex Leonard

It seems like an uncommon use case, but especially since `minimap2` can take gzipped references, this does (negligibly) complicate porting over to `pbmm2`.

If I subset the graph with `gfatools` (which doesn't include paths), the problem disappears. Manually adding the path back to the subgraph triggers the issue, so seems to be path-annotated...

Presumably some earlier mistake in handling the file. This should not happen (it is fair to assume R1/R2 are matched order), but it seems like something that could be flagged...

This was a big thread in #262. Even the ability to set args programatically (`workflow._singularity_args += `) seems to be not functioning the same as before. The singularity args seem...

>samtools import doesn't know what order the input reads are in at the point when it writes the header, but it will (at least in the case where you give...

>BWA does indeed require the entries in multiple input FASTQ This is actually what started the whole debacle, because QC'ing the "paired-end" reads with `fastp` went [fine](https://github.com/OpenGene/fastp/issues/632) and estimated all...