Nick Waters

Is there an official order of sections?

5

Not sure if this has been discussed elsewhere, but is there an official order that the different directives should be written? And if there is would it be possible to...

**Snakemake version** ``` $ snakemake --version 7.8.3 ``` **Describe the bug** It would be great to have some guidance on how workflow `container` directives are inheirited when importing workflows as...

add recreation script

27

Hi @zamaudio ! Thanks for writing a great tool. I needed to rescue some takes from a protools file, and wrote this python wrapper to make the sox commands to...

Issue with `-n` dry run

11

### Bug report info ```plain text act --bug-report act version: 0.2.31 GOOS: darwin GOARCH: amd64 NumCPU: 8 Docker host: DOCKER_HOST environment variable is unset/empty. Sockets found: /var/run/docker.sock Config files: /Users/nwaters/.actrc:...

Error building from source from pypi

2

Building from source from pypi fails with the following error: ``` /setup.py", line 43, in long_description=open("pypi_full.rst").read() FileNotFoundError: [Errno 2] No such file or directory: 'pypi_full.rst' ``` I think you just...

**Snakemake version** 8.4.2 **Describe the bug** As of PR #1407 fixing issue #1398, `SNAKEMAKE_PROFILE` cannot be passed to cluster jobs. We frequently used this as a required env variable to...

Bug in 7.32.4 trying to access outputs with the `rules` object: 'Namedlist' object has no attribute <x>

2

**Snakemake version** I experience this bug with snakemake 7.32.4, but not with 7.31.1 or prior versions. The versions in between (7.32.0, 7.32.1, etc) appear to have unrelated bugs that have...

Best practices for trimming, filtering, and host removal

2

Hi Kraken2 devs! I'm hoping to get some recommendations for best practices for the Kraken2 input fastqs. My questions are as follows: 1) should reads be trimmed before Kraken2? 2)...

Request -- use https://crates.io/crates/which for external command checking?

6

Hello! This is a bit of a strange request, but I am running into a strange error when running dockerized versions of CoverM. It is related to [this](https://discussion.fedoraproject.org/t/where-is-the-which-command-defined/62701) somehow, I...

Hi SPECTRA team! This PR is a small suggestion to add a status message after training to indicate that its ok if the model converges early. Since the the progress...