Leandro Hermida

`groups` and `group-components` are ignored on SLURM when defined in a profile YAML

1

**Snakemake version** 8.16 **Describe the bug** If I define `groups` and `group-components` in a profile yaml file they are ignored when using the SLURM executor. If I instead define them...

Service rules do not work with consumers that have wildcards (many instances of the consumer rule)

2

**Snakemake version** 8.16 **Describe the bug** Service rules do not work with consumers that use wildcards (many instances of the consumer rule) because resources are summed over all instances which...

**Snakemake version** 8.16.0 **Describe the bug** There is a common checkpoint use case where you have a set of `N` input files and for each input file a checkpoint will...

**Snakemake version** 8.16.0 **Describe the bug** `*_NUM_THREADS` env vars, e.g. `OMP_NUM_THREADS`, are not getting passed to `shell()` function calls inside a wrapper. I checked that in the wrapper `os.environ` has...

Why is `k2mask` set to use only half the number of available cores?

5

https://github.com/DerrickWood/kraken2/blob/4cbdc5fac92d0a19d76ce68d6633d7ff794a1587/scripts/k2#L485-L487

Make `k2` wrapper script available in `$PATH` in the Bioconda `kraken2` package

1

What I recently discovered is that some published Kraken2 functionality (https://github.com/DerrickWood/kraken2/issues/855) is only available if you run commands via the `k2` script, not the traditional binaries like `kraken2-build`. But the...

I'm not sure if it's already supported but does KrakenUniq support an interleaved paired-end FASTQ as input? Do I need the `--paired` flag with this input?