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MPUSP / nf-core-crispriscreen

Process next generation sequencing data obtained from CRISPRi repression library screenings
MIT License
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replace existing R containers with a version that is more complete #8

Closed m-jahn closed 1 year ago

m-jahn commented 2 years ago

Description of the bug

Currently two modules, FITNESS and RMARKDOWNNOTEBOOK require default containers that are rather incomplete, because they either lack DESeq2, or basic tidyverse packages like dplyr, tidyr, or other dependencies. On the fly installation in singularity is cumbersome and faulty. Better soution is to have a clean R + tidyverse + bioconductor container that works for all.

Command used and terminal output

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Relevant files

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System information

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m-jahn commented 1 year ago

The current solution is to use conda environments to fetch the required R packages. A container might be an option in the future but is too much work currently. Closed with e734c2c1b6e61516807278f58042f3e53dfa3187.