From 40384ac3df03629a10a3c10a6f12d49ac98c9618 Mon Sep 17 00:00:00 2001 From: xies4 Date: Wed, 1 May 2024 11:16:15 -0400 Subject: [PATCH] Update dev_w_docker.md --- docs/dev_w_docker.md | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/docs/dev_w_docker.md b/docs/dev_w_docker.md index af02a80..5f14f95 100644 --- a/docs/dev_w_docker.md +++ b/docs/dev_w_docker.md @@ -25,17 +25,16 @@ system(paste0('Rscript ', script_path, # %exclude_jupyterlab% 3. Write the main code -First, read the options using readRDS: +After capturing the options, read them using `readRDS()` and proceed with the main code: ``` opt = readRDS("/Volumes/ccrsf-static/Analysis/xies4/github_repos/pipeline_dev_test/singleR/opt.rds") # %exclude_jupyterlab% +# main code goes here ``` -Then include the code to accomplish the task. - 4. Generate production script: `sc_singleR.prod.R` -The code below will first convert the `ipynb` file to a script file and combine the script for option `sc_singleR_opt.R` and `sc_singleR.r` (output file of `jupyter nbconvert -`) with exclusion of the lines with "exclude_jupyterlab". +Combine the necessary scripts and exclude irrelevant lines marked with `exclude_jupyterlab` to create the production script: ``` notebook_prefix = "sc_singleR" # %exclude_jupyterlab%