From 9272fc4170a87cac295d407c3292b0998a3c51c5 Mon Sep 17 00:00:00 2001 From: alvaannett <46521652+alvaannett@users.noreply.github.com> Date: Wed, 6 Sep 2023 11:53:49 -0400 Subject: [PATCH] Update README.md --- README.md | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 65536b6..e925afb 100644 --- a/README.md +++ b/README.md @@ -350,9 +350,9 @@ Add table with resource usage for different sice references and queries # :woman_mechanic: Adding new tools -1. Identify new tool +**1. Identify new tool** -2. Read documentation. Try to find this information: +**2. Read documentation. Try to find this information:** - Can tool be split into training and prediction step? - What normalization does the tool expect for the reference and query? - Can the tool be paralellized? How? @@ -360,22 +360,26 @@ Add table with resource usage for different sice references and queries - Are there extra outputs from the training and prediction that may be usefull to save (qc plots, probbability/p-value associated with each prediction etc..)? - Are there parameters in the training and prediction that can be changed? What are the defult values? -3. Open issue and create a branch from dev with the tool name + your name +**3. Open issue and create a branch from dev with the tool name + your name** -4. Write scripts (check Templats folder for how to structure scripts: [Templats](Templats)) +**4. Write scripts (check Templats folder for how to structure scripts: [Templats](Templats))** - The scripts should take the reference expression/labels and query expression .csv files as specified in [Prepare reference](#2-prepare-reference) and [Prepare query samples](#3-prepare-query-samples) - The scripts should take any additional parameters you want to be able to change as input -5. Update the snakefiles with rules for the new tool (ask Alva if you need help) +**5. Update the snakefiles with rules for the new tool (ask Alva if you need help)** -6. Update README +**6. Update README** - Write detailed documentation about the tool in the section: [Detailed documentation on tool wrapper scripts](female-detective-detailed-documentation-on-tool-wrapper-scripts) - Detailed documentation should include information from step 2 and if you changed any default parameters/normalization etc.. Links to papers and tutorials used to create the scripts can be put here. - Update other sections of the readme such as the [Installation and Dependencies](gear-installation-and-dependencies) and [Available tools](hammer-and-wrench-available-tools) -7. Create pull request from your branch to dev and request reviewer +**7. Create pull request from your branch to dev and request reviewer** -8. Make sure module on Narval/Hydra gets updated with necessary packages +**8. When pull request is approved merge with dev** +- Rebase with dev +- Squash + merge + +**9. Make sure module on Narval/Hydra gets updated with necessary packages** # 🐍 Snakemake Tips and Tricks