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formbio / laava

LAAVA: Long-read AAV Analysis
MIT License
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Remove bin/ scripts in favor of native Nextflow and Python packaging #49

Open etal opened 3 months ago

etal commented 3 months ago

The scripts implementing each Nextflow process are written in Bash and stored under the bin/ directory for execution. This complicates maintenance and portability a little bit; it would be better to consolidate all relevant logic under src/, install it in the Docker environment as a single package, and put the remaining (simple) commands directly in the script block of each Nextflow process.

Blocked by #19, the main source of complexity in the scripts.

etal commented 2 weeks ago

Partially addressed in #53 -- the shell scripts called directly by each Nextflow process now live under src/, but they were not ported to Python/Nextflow/Groovy in that PR.