Merge branch 'main' into rfcs/chipseq_workflow

.github/workflows/deploy.yml

@@ -3,24 +3,31 @@ name: Continuous Deployment
 on:
   push:
     branches:
-      - master
+      - main 
       - rfcs/*
 
 jobs:
   deploy:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     steps:
-      - uses: actions/checkout@v2
+      # (1) Check out the repository
+      - uses: actions/checkout@v3
+
+      # (2) Install `mdbook`
       - name: Install Dependencies
         uses: peaceiris/actions-mdbook@v1
         with:
           mdbook-version: "latest"
+
+      # (3) Build the documentation
       - run: bash bin/ci-build.sh
+
+      # (4) Deploy the documentation to GitHub pages
       - name: Deploy
         uses: peaceiris/actions-gh-pages@v3
         with:
-          deploy_key: ${{ secrets.ACTIONS_DEPLOY_KEY }}
+          github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./book
           user_name: "St. Jude Cloud"
           user_email: support@stjude.cloud
-          commit_message: "Deployed from ${{ github.event.head_commit.message }}"
+          commit_message: "Deployed from ${{ github.event.head_commit.message }}"

.typo-ci.yml

@@ -14,4 +14,5 @@ excluded_words:
   - sampe
   - Bowtie
   - stjude
-  - chipsummitdb-
+  - chipsummitdb-
+  - epigenetic

README.md

@@ -1,8 +1,6 @@
 <p align="center">
-  <a href="https://github.com/stjudecloud/rfcs"><img src="https://github.com/stjudecloud/rfcs/raw/master/docs/rfcs-banner-blueprint.jpg" width="800" title="St. Jude Cloud RFCs"></a>
-  <a href="https://actions-badge.atrox.dev/stjudecloud/rfcs/goto"><img alt="Build Status" src="https://img.shields.io/endpoint.svg?url=https%3A%2F%2Factions-badge.atrox.dev%2Fstjudecloud%2Frfcs%2Fbadge&style=flat" /></a>
-  <a href="https://gitter.im/stjudecloud/rfcs?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge" target="_blank">
-    <img alt="Gitter: RFCs" src="https://badges.gitter.im/stjudecloud/rfcs.svg" />
+  <a href="https://github.com/stjudecloud/rfcs"><img src="https://github.com/stjudecloud/rfcs/raw/main/docs/rfcs-banner-blueprint.jpg" width="800" title="St. Jude Cloud RFCs"></a>
+  <a href="https://github.com/stjudecloud/rfcs/actions/workflows/deploy.yml"><img alt="Build Status" src="https://github.com/stjudecloud/rfcs/actions/workflows/deploy.yml/badge.svg" /></a>
   </a>
 </p>
 
@@ -80,13 +78,13 @@ python3 -m http.server -d book
 
 ## Contributing
 
-Contributions, issues and feature requests are welcome!<br />Feel free to check [issues page](https://github.com/stjudecloud/rfcs/issues). You can also take a look at the [contributing guide](https://github.com/stjudecloud/rfcs/blob/master/CONTRIBUTING.md).
+Contributions, issues and feature requests are welcome!<br />Feel free to check [issues page](https://github.com/stjudecloud/rfcs/issues). You can also take a look at the [contributing guide](https://github.com/stjudecloud/rfcs/blob/main/CONTRIBUTING.md).
 
 
 ## 📝 License
 
 Copyright © 2020 [St. Jude Cloud Team](https://github.com/stjudecloud).<br />
-This project is [MIT](https://github.com/stjudecloud/rfcs/blob/master/LICENSE.md) licensed.
+This project is [MIT](https://github.com/stjudecloud/rfcs/blob/main/LICENSE.md) licensed.
 
 ## Questions
 

bin/ci-build.sh

@@ -42,15 +42,15 @@ git fetch --all
 BRANCHES=()
 while IFS= read -r line; do
     BRANCHES+=( "$line" )
-done < <( git branch --list --all | sed 's,\*,,g' | xargs -n1 | grep "remotes/origin" | sed 's,remotes/origin/,,g' | sort | uniq | grep -e 'master' -e 'rfcs/' )
+done < <( git branch --list --all | sed 's,\*,,g' | xargs -n1 | grep "remotes/origin" | sed 's,remotes/origin/,,g' | sort | uniq | grep -e 'main' -e 'rfcs/' )
 
 echo "== Creating Drafts File =="
 printf "# Drafts\n\n" > "${DRAFTS_FILE}"
 echo "The following are _candidate_ RFCs that are being rendered for easy review. They are *not* accepted St. Jude Cloud RFCs. For more information please see [the associated pull request](https://github.com/stjudecloud/rfcs/pulls)." >> "${DRAFTS_FILE}"
 printf "\n\n" >> "${DRAFTS_FILE}"
 
 for CURRENT_BRANCH in "${BRANCHES[@]}"; do
-  if [[ "${CURRENT_BRANCH}" != "master" ]]; then
+  if [[ "${CURRENT_BRANCH}" != "main" ]]; then
     echo "- [${CURRENT_BRANCH}](https://stjudecloud.github.io/rfcs/branches/$CURRENT_BRANCH)" >> "${DRAFTS_FILE}"
   fi
 done
@@ -59,7 +59,7 @@ done
 echo "== Build RFC Branches =="
 for CURRENT_BRANCH in "${BRANCHES[@]}"; do 
   BRANCH_DIR="${BOOK_DIR}/branches/${CURRENT_BRANCH}"
-  if [[ "${CURRENT_BRANCH}" == "master" ]]; then
+  if [[ "${CURRENT_BRANCH}" == "main" ]]; then
     BRANCH_DIR="${BOOK_DIR}/"
   fi
   build "${CURRENT_BRANCH}" "${BRANCH_DIR}" "${DRAFTS_FILE}"

text/0001-rnaseq-workflow-v2.0.0.md

@@ -1,4 +1,4 @@
-# Table of Contents <!-- omit in toc -->
+# RNA-Seq v2 Pipeline <!-- omit in toc -->
 
 - [Introduction](#introduction)
 - [Motivation](#motivation)
@@ -58,7 +58,7 @@ First, we researched what some of the projects we respect in the community are d
 [gencode-v24]: https://www.gencodegenes.org/human/release_24.html
 [gencode-v26]: https://www.gencodegenes.org/human/release_26.html
 
-**Note:** You can confirm which patch the GENCODE genesets is based on just by clicking on the hyperlink. Verifying that each of these reference genomes is really based on `GRCh38_no_alt` takes a little bit more elbow grease: if you're interested, you can check out the comparison table [in the appendix](#reference-genome-comparison). If you are _really_ interested, you can recapitulate those results by running [the associated Jupyter notebook](https://github.com/stjudecloud/rfcs/tree/master/resources/0001-rnaseq-workflow-v2.0.0/GenomeComparison.ipynb).
+**Note:** You can confirm which patch the GENCODE genesets is based on just by clicking on the hyperlink. Verifying that each of these reference genomes is really based on `GRCh38_no_alt` takes a little bit more elbow grease: if you're interested, you can check out the comparison table [in the appendix](#reference-genome-comparison). If you are _really_ interested, you can recapitulate those results by running [the associated Jupyter notebook](https://github.com/stjudecloud/rfcs/tree/main/resources/0001-rnaseq-workflow-v2.0.0/GenomeComparison.ipynb).
 
 Based on the results of the above investigation, I reached out to the author of STAR, Alex Dobin, to get his opinion on whether the differences might affect some results. You can read my question and his reply [here](https://github.com/alexdobin/STAR/issues/673). In short, he confirms that, yes, this may alter results for the various analysis types we were interested in.
 
@@ -285,7 +285,7 @@ Below are the results of an analysis of each pipeline's `GRCh38`-based reference
 3. Use `picard CreateSequenceDictionary` to get the md5sums for each sequence in the dictionary.
 4. Compare for the common chromosomes in each reference (the autosomes, the sex chromosomes, and the EBV decoy).
 
-If you are interested in seeing the _full_ comparison table or in regenerating these results, you can see [the associated Jupyter notebook](https://github.com/stjudecloud/rfcs/tree/master/resources/0001-rnaseq-workflow-v2.0.0/GenomeComparison.ipynb).
+If you are interested in seeing the _full_ comparison table or in regenerating these results, you can see [the associated Jupyter notebook](https://github.com/stjudecloud/rfcs/tree/main/resources/0001-rnaseq-workflow-v2.0.0/GenomeComparison.ipynb).
 
 | Sequence Name | NCBI (baseline)                    | ENCODE                             | GDC                                | TOPMed                             | Concordant |
 | ------------- | ---------------------------------- | ---------------------------------- | ---------------------------------- | ---------------------------------- | ---------- |

text/0002-scRNA-Seq-workflow.md

@@ -1,4 +1,4 @@
-# Table of Contents <!-- omit in toc -->
+# scRNA-Seq Pipeline <!-- omit in toc -->
 
 - [Introduction](#introduction)
 - [Motivation](#motivation)
@@ -35,7 +35,7 @@ For consistency with other St. Jude Cloud datasets, we are not considering psued
 
 [Bruning, et. al.](https://doi.org/10.1093/gigascience/giac001) (2022) provide a useful comparison of commonly used scRNA-Seq methods. However due to our preference for an alignment-based method, we will choose between Cell Ranger and STARsolo. Cell Ranger is the most commonly used method for processing data generated from the 10x protocol. Downstream analysis tools have been developed to directly ingest data in the formats produced by Cell Ranger. The tool is an integrated system that performs alignment, feature counting, and quality control.
 
-<img src="../resources/0002-scRNA-Seq-workflow/aligner_comparison.jpeg" width="800">
+<img src="/rfcs/resources/0002-scRNA-Seq-workflow/aligner_comparison.jpeg" width="800">
 
 ### Quantification choice