diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index cbe4e4f..5004986 100644 --- a/.github/workflows/deploy.yml +++ b/.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 }}" \ No newline at end of file diff --git a/.typo-ci.yml b/.typo-ci.yml index e6bec9f..86186ea 100644 --- a/.typo-ci.yml +++ b/.typo-ci.yml @@ -14,4 +14,5 @@ excluded_words: - sampe - Bowtie - stjude - - chipsummitdb- \ No newline at end of file + - chipsummitdb- + - epigenetic diff --git a/README.md b/README.md index 5d3121b..2730fae 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,6 @@

- - Build Status - - Gitter: RFCs + + Build Status

@@ -80,13 +78,13 @@ python3 -m http.server -d book ## Contributing -Contributions, issues and feature requests are welcome!
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!
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).
-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 diff --git a/bin/ci-build.sh b/bin/ci-build.sh index 9ab6bcf..430203c 100755 --- a/bin/ci-build.sh +++ b/bin/ci-build.sh @@ -42,7 +42,7 @@ 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}" @@ -50,7 +50,7 @@ echo "The following are _candidate_ RFCs that are being rendered for easy review 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}" diff --git a/text/0001-rnaseq-workflow-v2.0.0.md b/text/0001-rnaseq-workflow-v2.0.0.md index 1709562..a6a835e 100644 --- a/text/0001-rnaseq-workflow-v2.0.0.md +++ b/text/0001-rnaseq-workflow-v2.0.0.md @@ -1,4 +1,4 @@ -# Table of Contents +# RNA-Seq v2 Pipeline - [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 | | ------------- | ---------------------------------- | ---------------------------------- | ---------------------------------- | ---------------------------------- | ---------- | diff --git a/text/0002-scRNA-Seq-workflow.md b/text/0002-scRNA-Seq-workflow.md index 39878b1..aced0a1 100755 --- a/text/0002-scRNA-Seq-workflow.md +++ b/text/0002-scRNA-Seq-workflow.md @@ -1,4 +1,4 @@ -# Table of Contents +# scRNA-Seq Pipeline - [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. - + ### Quantification choice