Charlie
Charlie
Hi all, coming back to this 3.5 years later, I've got a PR #408 that adds the desired clean_decontam target. I'm wondering though if it would be better to instead...
From the responses I've gotten asking users about this, it sounds like this won't be a very heavily used feature either way it's implemented. I'll merge the PR to add...
Closing this now, the filtering implemented in [sbx_mapping](https://github.com/sunbeam-labs/sbx_mapping) should accomplish the same end.
Hi all, I'm closing this issue for inactivity. If the problem resurfaces with the latest version of sunbeam and the sbx_kraken extension, please file a new issue under the [sbx_kraken...
Closing this issue for inactivity. As for the `conda env config vars` update I suggested, I'd rather maintain backwards compatibility than have this minor convenience.
Hi @tuhina3184, I'm closing this for inactivity. I'd recommend using sunbeam 4 which was just released and fixes a lot of bugs similar to this one.
Hi again @levlitichev, I think a lot of what you mentioned has now been integrated into sunbeam as of the latest v4.0.0 release. I'm going to close this issue but...
Update, the problem is that the conda envs within the singularity images aren't being activated. If I go into the container and manually activate the environment or include the bin/...
I found what's going wrong here: I'm using `containerized: ...` in the workflow but then running it with `--sdm apptainer` where apparently it needs `--sdm conda apptainer` so that it...
Looked a bit further into it. It should be raising [this exception](https://github.com/snakemake/snakemake-interface-common/blob/2e3fdb644846288926a07cd6691fae177e82ec3f/snakemake_interface_common/plugin_registry/__init__.py#L46) but instead the try/catch block [here](https://github.com/snakemake/snakemake/blob/41994827338381b7c1434a55f619dde354d4e6b0/snakemake/cli.py#L2135C29-L2135C29) gets caught on the preceding `parse_args` line [here](https://github.com/snakemake/snakemake/blob/41994827338381b7c1434a55f619dde354d4e6b0/snakemake/cli.py#L706). Could it maybe be...