Bugfix/several runtime issues #46
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…docker Unifre mount issue with docker.
Dev -> main for release v1.3
…nder. These tools are very picky with the tmp directory, so I've implemented a workaround using a "tmp" directory in the process workdir.
- Removed the custom python container with a seqera container one (retry and requests) - Removed the custom python container with the biocontainers python one when possible - Added the singularity image to the containers on those modules that was possible - Added ruff, black and some other base pre-commit - Migrated the python unit tests to pytest and fixed them - Ran ruff and black on the scripts I am testing all this ATM.
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Our .gitignore is more comprehensive than the nf-core template one
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Fixed some runtime issues with Prokka, AMRFinder, and CRISPRCasFinder.
The problem with CRISPRCasFinder was that it attempted to mv files while the app was still running, had the file open, or while the shared filesystem was still using the file. I forked the repository and replaced the mv statements with cp, which resolved the issue. I will submit a PR to the repository. In the meantime, we will need to rely on a custom container I've built.
This update also includes changes to the linting tools and pre-commit configurations.
PR checklist
nf-core lint).