Add nf use-case to docs

docs/pipelines.md

@@ -0,0 +1,15 @@
+# Pipelines
+
+Pipelines (sometimes also called workflows) in bioinformatics encompass structured sequences of computational tools that manipulate, visualize, and potentially interpret biological data, orchestrating a coherent analytical framework. Prominent workflow managers such as Snakemake, Nextflow, and Redun offer advanced tools for orchestrating, executing, and overseeing the execution of these pipelines, addressing challenges related to version control, collaborative research efforts, and efficient resource utilization.
+
+Lamin enables tracking of pipeline execution including metadata such as name or version.
+Moreover, it tracks data lineage as it flows through pipelines and validates output against biological registries and ontologies.
+
+The following notebooks entail example runs of various workflow managers and their interaction with Lamin.
+
+```{toctree}
+:maxdepth: 1
+
+../redun
+../nextflow
+```

noxfile.py

@@ -30,7 +30,7 @@ def install(session: nox.Session) -> None:
 ../data-lineage
 ../by-registry
 ../by-datatype
-../redun
+pipelines
 ```
 """
 
@@ -101,12 +101,19 @@ def pull_artifacts(session):
     for path in Path("lamindb_docs/faq").glob("*"):
         path.rename(Path("docs/faq") / path.name)
     replace_content("docs/faq.md", {FAQ_MATCH: FAQ_APPEND})
+
     # lamindb guide
     replace_content("docs/guide.md", {OTHER_TOPICS_ORIG: "\n\n"})
-    # integrations
+
+    # workflows
     pull_from_s3_and_unpack("redun_lamin_fasta_docs.zip")
     Path("redun_lamin_fasta_docs/redun.ipynb").rename("docs/redun.ipynb")
-    # usescases
+    pull_from_s3_and_unpack("nextflow_lamin_usecases_docs.zip")
+    Path("nextflow_lamin_usecases_docs/guide/bulk_rna_seq.ipynb").rename(
+        "docs/nextflow.ipynb"
+    )
+
+    # use-cases
     pull_from_s3_and_unpack("lamin_usecases_docs.zip")
     for path in Path("lamin_usecases_docs/").glob("*"):
         if (