updating README, shell script, nextflow pipeline, and R environment#9
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graceakatsu wants to merge 24 commits intogreenelab:mainfrom
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updating README, shell script, nextflow pipeline, and R environment#9graceakatsu wants to merge 24 commits intogreenelab:mainfrom
graceakatsu wants to merge 24 commits intogreenelab:mainfrom
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…ata script to match the new numbering
…e loading conda environment and ensuring download of nextflow
…to message out how many .zip and .gz files and unzipped if any
…ude new R unzipping script, adding .Rprofile and renv/.gitignore
graceakatsu
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ivichadriana
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Jun 18, 2025
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unzipping file removed, conda environment details removed.
is the goal to have every single file exclusively in R? if so, the subsequent files i am creating for my analysis will not work.
…ing the optional unzipping script from the nextflow
updating readme slightly to reflect new format of run_pipeline.sh
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updating pipeline based on conversation (and also after a conversation with kevin from HPC) - both R and python environments should now be working harmoniously, and the pipeline should be able to be successfully run both on HPC and locally :) PR now ready for review! |
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these updates make the environment and pipeline reproducible and able to be run from one shell script.