From b260fe80061928800fda1e42117948355eb6b0a0 Mon Sep 17 00:00:00 2001
From: slsevilla <slsevilla@gmail.com>
Date: Mon, 8 Jan 2024 16:44:28 -0500
Subject: [PATCH] create zenodo page

---
 docs/OtherHowTos/zenodo.md | 73 ++++++++++++++++++++++++++++++++++++++
 docs/index.md              |  1 +
 mkdocs.yml                 |  1 +
 3 files changed, 75 insertions(+)
 create mode 100644 docs/OtherHowTos/zenodo.md

diff --git a/docs/OtherHowTos/zenodo.md b/docs/OtherHowTos/zenodo.md
new file mode 100644
index 0000000..01754dd
--- /dev/null
+++ b/docs/OtherHowTos/zenodo.md
@@ -0,0 +1,73 @@
+# Zenodo
+
+Submit a pipeline to Zenodo in order to create a DOI for publication.
+
+## Reference link
+
+Use the link for full information, summarized below: https://www.youtube.com/watch?v=A9FGAU9S9Ow
+
+## Prepare GitHub Repository
+
+The GitHub repository should include the following:
+
+1. README page
+2. Documentation page, such as mkdocs, with usage and contact information
+3. Tagged and versioned, stable repository
+
+## Link GitHub account to Zenodo
+
+1. Go to [Zenodo](https://zenodo.org/)
+
+2. Select `username` in the top right >> `Profile`. Select `GitHub``
+
+3. Click `Sync Now` (top right) to update repos. NOTE: You may have to refresh the page
+
+4. Toggle the `On` button on the repo you wish to publish. This will move the pipeline to the `Enable Repositories` list.
+
+## Prepare GitHub Repo
+
+1. Go to [GitHub](https://www.github.com) and find the repository page.
+
+2. Select `Releases` >> `Draft a new release`
+
+3. Create a tag, following naming semantics described [here](https://ccbr.github.io/HowTos/GitHub/sop_projpipes/#release-tagged-nomenclature)
+
+4. Describe the tag with the following: "Connecting pipeline to Zenodo"
+
+## Update Zenodo Information
+
+1. Go to [Zenodo](https://zenodo.org/)
+
+2. Select `My dashboard` >> `Edit`
+
+3. Update the following information:
+
+- Resource Type: Software
+- Title: Full Pipeline Name (ShorthandName) (IE Mouse nEoanTigen pRedictOr (METRO)
+- Creators: Add creators, including ORCID's whenever possible
+- Description: A short description of the main features of the pipeline
+- Additional Description: If you use this software, please cite it as below.
+- Keywords and subjects: Add several keywords related to the pipeline
+- Version: add the version used in GitHub
+- Publisher: Zenodo
+- Related works: "Is original form of" "github website" URL 
+
+4. Select the Zenodo release
+
+- Scroll to the bottom right, under `Export`, select `Citation File Format` and `Export`.
+
+## Add DOI, citation to GitHub
+
+1. Go to [Zenodo](https://zenodo.org/)
+
+2. Select `username` in the top right >> `Profile`. Select `GitHub``
+
+3. Click `Sync Now` (top right) to update repos. NOTE: You may have to refresh the page
+
+4. Copy the DOI for the repository
+
+5. Return to the GitHub repository and edit the `README` of the GitHub repo, adding the DOI link.
+
+6. Create a new file `CITATION.cff`. Paste the exported `cff` file. 
+
+7. Create a new tagged version. 
\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
index 0a9bc25..099f678 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -7,6 +7,7 @@ You'll find how-to-guides, best practices and tutorials under the following page
     - How To: Create UCSC Tracks
     - How To: Create an R package
     - How To: use Datashare
+    - How To: Create a Zenodo DOI Link
     - Tutorials: Snakemake
     
 This page was created through the [contributions](https://ccbr.github.io/HowTos/contributions/) of several members within [CCBR](https://bioinformatics.ccr.cancer.gov/ccbr/). If you would like to contribute to it's development, please email [Samantha Sevilla](mailto:samantha.sevilla@nih.gov).
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
index 78ec494..51f7054 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -126,6 +126,7 @@ nav:
     - Troubleshooting: Rpackage/common_issues.md
   - Other How Tos:
       - Datashare: OtherHowTos/datashare.md
+      - Zenodo: OtherHowTos/zenodo.md
   - Tutorials:
     - Snakemake: Tutorials/snakemake.md
   - Contributions: contributions.md