Sam Nicholls

https://docs.python.org/3/library/resource.html

Hi @BioWilko, fancy seeing you here! I believe I have narrowed down the scope of this issue to a slicing operation in `join_samples`. I have crafted a dummy HDF5 file...

Your data triggered an interesting edge case wherein the Sample chunk generator was emitting a chunk containing only a long insertion. Compared against the reference the chunk had only one...

Does `merge` offer this option now?

As a workaround for yourself, could you increase the RAM allowance for samtools sort (with -m 1500M or -m 2G, for example) such that there are fewer (larger) temp files...

Should it be the case that `source` and `dest` are set to `pw.Dir` after `user.CurrentOriginal` returns an `err`? https://github.com/sylabs/singularity/blob/377e2786b69315edc2820dbc0a89632141450503/internal/pkg/runtime/engine/singularity/container_linux.go#L1611-L1613

I don't have an appropriate good before/after to hand, so if you've got some automated testing ready to go and you're happy to run it that would be great! 😇

Hi @mirpedrol! I think if this were to get added to the template it should be all-or-nothing to ensure it provides predictable behaviour. That is, we should either add it...

For what it's worth, pipelines cannot use their own `--version` with the template as it stands anyway, as it will abort the pipeline with the following message: ``` ERROR: You...

We're seeing something similar with one of our PhD students too. She's aligning a ~1.6 GB FASTQ to a set of 16S references (n=~21000, 50Mb). The job slowly but surely...