Update changelog for v4.2.0 (#64)

* Update changelog for v4.2.0 * Update pigeon version 1.3.0 --------- Co-authored-by: Jessica Mattick <[email protected]>
PacificBiosciences · Oct 29, 2024 · 8d9047b · 8d9047b
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diff --git a/docs/changelog.md b/docs/changelog.md
@@ -5,7 +5,12 @@ nav_order: 99
 ---
 
 # Version changelog
- * **4.1.0**
+ * **4.2.0**
+   * SMRT Link v25.1 release
+   * Update `PM` to show platform name
+   * Update `RGID` to match `molecule` read name for `groupdedup` / `dedup`
+
+ * 4.1.0
    * Update minimap2 to version 2.26
    * SMRT Link v13.0 release
 

diff --git a/docs/classification/pigeon-changelog.md b/docs/classification/pigeon-changelog.md
@@ -7,7 +7,15 @@ nav_order: 99
 
 # Pigeon version changelog
 
-**1.1.0**
+**1.3.0**
+   * SMRT Link v25.1 release
+   * Add `exclude-singletons` option to `report`
+
+1.2.0
+   * SMRT Link v13.0 release
+   * Improved record validation messages
+
+1.1.0
    * Multi-sample support
    * Add `prepare` tool
    * Bug fixes

diff --git a/docs/classification/pigeon.md b/docs/classification/pigeon.md
@@ -36,4 +36,4 @@ The CLI workflow is described [here](/classification/workflow).
 The latest version of `pigeon` is distributed through [BioConda](https://github.com/PacificBiosciences/pbbioconda).
 
 ## Versions
-Version **1.1.0**: [Full changelog here](/classification/pigeon-changelog)
+Version **1.3.0**: [Full changelog here](/classification/pigeon-changelog)
diff --git a/docs/classification/workflow.md b/docs/classification/workflow.md
@@ -125,6 +125,12 @@ Gene and isoform- level saturation can be determined by subsampling the classifi
 pigeon report <classification.filtered_lite_classification.txt> <saturation.txt>
 ```
 
+For bulk Iso-Seq that has been clustered using `cluster2`, use the `--exclude-singletons` option.
+
+``
+pigeon report --exclude-singletons <classification.filtered_lite_classification.txt> <saturation.txt>
+```
+
 ### Make Seurat-compatible gene- and isoform- count matrix for single-cell Iso-Seq
 
 Output files that are compatible with the downstream [Seurat](https://satijalab.org/seurat/) analysis package.

diff --git a/docs/index.md b/docs/index.md
@@ -28,7 +28,7 @@ Please refer to our [official pbbioconda page](https://github.com/PacificBioscie
 for information on Installation, Support, License, Copyright, and Disclaimer.
 
 ## Latest Version
-Version **4.0.0**: [Full changelog here](/changelog)
+Version **4.2.0**: [Full changelog here](/changelog)
 
 ## What's new!
 Version 4.0 adds a new `cluster2` tool that enables clustering of hundreds of