add documentation for cytof assay plugin (#1711)

bihealth · Jul 20, 2023 · ca37751 · ca37751
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diff --git a/docs_manual/source/dev_apps.rst b/docs_manual/source/dev_apps.rst
@@ -220,6 +220,8 @@ within assays based on the assay type. They are placed under
 
 The following assay sub-apps currently exist:
 
+cytof
+    Protein expression profiling / mass cytometry assay app.
 dna_sequencing
     DNA sequencing assay app.
 generic_raw

diff --git a/docs_manual/source/metadata_advanced.rst b/docs_manual/source/metadata_advanced.rst
@@ -91,6 +91,7 @@ SODAR currently supports the following assay plugins:
 - **Metabolite Profiling / Mass Spectrometry**
 - **Microarray**
 - **Protein Expression Profiling / Mass Spectrometry**
+- **Protein Expression Profiling / Mass Cytometry**
 
 Common links as well as plugin specific links are detailed below.
 
@@ -182,3 +183,21 @@ Protein Expression Profiling / Mass Spectrometry Plugin
     * Files are linked to ``RawData`` under the assay.
 - Used with measurement type / technology type
     * protein expression profiling / mass spectrometry
+
+Protein Expression Profiling / Mass Cytometry Plugin
+-------------------------------------------------------
+
+- Internal name: ``samplesheets_assay_cytof``
+- Additional assay shortcuts
+    * N/A
+- Row-specific links
+    * Rows with an **Assay Name** set in the **mass cytometry** process are
+      linked to ``{Assay Name}`` to created one collection per measurement run.
+- Inline links
+    * *Barcode key* and *Antibody panel* process parameter values are linked
+      to ``MiscFiles``
+    * *Report file* process parameter/comment values are linked
+      to ``{Assay Name}``
+    * *Raw Data Files* and *Derived Data Files* are linked to ``{Assay Name}``
+- Used with measurement type / technology type
+    * protein expression profiling / mass cytometry