Merge pull request #12 from NIGMS/Update-Links

Update links and Reusable Workflows

.github/workflows/check-links.yaml

@@ -0,0 +1,13 @@
+name: 'Check Links'
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+
+jobs:
+  link_check:
+    name: 'Link Check'
+    uses: NIGMS/NIGMS-Sandbox/.github/workflows/check-links.yaml@main
+    with:
+      repo_link_ignore_list: ""

.github/workflows/notebook-lint.yaml

@@ -0,0 +1,14 @@
+name: 'Lint Notebook'
+on:
+  push:
+  workflow_dispatch:
+permissions:
+  contents: write
+  id-token: write
+
+jobs:
+  lint:
+    name: 'Linting'
+    uses: NIGMS/NIGMS-Sandbox/.github/workflows/notebook-lint.yaml@main
+    with:
+      directory: .

ATACseq_BonusTutorial.ipynb

@@ -95,7 +95,7 @@
    "id": "341b0313-dbb9-4f0b-b6db-11f02ffe15ac",
    "metadata": {},
    "source": [
-    "We are going to pull a new dataset from SRA. In this example, we are going to use data from an experiment that compared cis-regulatory elements across tissues in zebrafish. The BioProject ID is [PRJNA553572](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA553572). There are over 200 samples in this experiment, but for simplicity, we are only going to use one liver sample and one muscle sample. The accession numbers for these samples are SRR12173474 and SRR12173476. To learn how to pull data from SRA, we recommend you consult the [STRIDES tutorial on SRA downloads](https://github.com/STRIDES/NIHCloudLabGCP/blob/main/tutorials/notebooks/SRADownload/SRA-Download.ipynb). For this situation, we have already pulled the data from SRA and have it in our storage bucket, so we will copy it to our directory."
+    "We are going to pull a new dataset from SRA. In this example, we are going to use data from an experiment that compared cis-regulatory elements across tissues in zebrafish. The BioProject ID is [PRJNA553572](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA553572). There are over 200 samples in this experiment, but for simplicity, we are only going to use one liver sample and one muscle sample. The accession numbers for these samples are SRR12173474 and SRR12173476. To learn how to pull data from SRA, we recommend you consult the [STRIDES tutorial on SRA downloads](https://github.com/STRIDES/NIHCloudLabGCP/blob/main/notebooks/SRADownload/SRA-Download.ipynb). For this situation, we have already pulled the data from SRA and have it in our storage bucket, so we will copy it to our directory."
    ]
   },
   {