changelog updates

broadinstitute · Sep 24, 2024 · 5b380ae · 5b380ae
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diff --git a/pipelines/skylab/multiome/Multiome.changelog.md b/pipelines/skylab/multiome/Multiome.changelog.md
@@ -1,3 +1,7 @@
+# 5.7.0
+2024-09-24 (Date of Last Commit)
+* Added a python implementation of DoubletFinder to calculate to doublet scores in gene expression data; percent doublets are now available as a library-level metric and individual doublet scores for cell barcodes are in the h5ad
+
 # 5.6.1
 2024-09-11 (Date of Last Commit)
 * Updated warp-tools docker which added create_h5ad_snss2.py to the docker image. This change does not affect the Multiome pipeline

diff --git a/pipelines/skylab/multiome/Multiome.wdl b/pipelines/skylab/multiome/Multiome.wdl
@@ -9,7 +9,7 @@ import "../../../tasks/broad/Utilities.wdl" as utils
 
 workflow Multiome {
 
-    String pipeline_version = "5.6.1"
+    String pipeline_version = "5.7.0"
 
 
     input {

diff --git a/pipelines/skylab/optimus/Optimus.changelog.md b/pipelines/skylab/optimus/Optimus.changelog.md
@@ -1,3 +1,7 @@
+# 7.7.0
+2024-09-24 (Date of Last Commit)
+
+* Added a python implementation of DoubletFinder to calculate to doublet scores in gene expression data; percent doublets are now available as a library-level metric and individual doublet scores for cell barcodes are in the h5ad
 # 7.6.1
 2024-09-11 (Date of Last Commit)
 * Updated warp-tools docker which added create_h5ad_snss2.py to the docker image. This change does not affect the Optimus pipeline

diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl
@@ -71,7 +71,7 @@ workflow Optimus {
   # version of this pipeline
 
 
-  String pipeline_version = "7.6.1"
+  String pipeline_version = "7.7.0"
 
 
   # this is used to scatter matched [r1_fastq, r2_fastq, i1_fastq] arrays

diff --git a/pipelines/skylab/paired_tag/PairedTag.changelog.md b/pipelines/skylab/paired_tag/PairedTag.changelog.md
@@ -1,3 +1,7 @@
+# 1.7.0
+2024-09-24 (Date of Last Commit)
+* Added a python implementation of DoubletFinder to calculate to doublet scores in gene expression data; percent doublets are now available as a library-level metric and individual doublet scores for cell barcodes are in the h5ad
+
 # 1.6.1
 2024-09-11 (Date of Last Commit)
 * Updated warp-tools docker which added create_h5ad_snss2.py to the docker image. This change does not affect the PairedTag pipeline

diff --git a/pipelines/skylab/paired_tag/PairedTag.wdl b/pipelines/skylab/paired_tag/PairedTag.wdl
@@ -8,7 +8,7 @@ import "../../../tasks/broad/Utilities.wdl" as utils
 
 workflow PairedTag {
 
-    String pipeline_version = "1.6.1"
+    String pipeline_version = "1.7.0"
 
 
     input {

diff --git a/pipelines/skylab/slideseq/SlideSeq.changelog.md b/pipelines/skylab/slideseq/SlideSeq.changelog.md
@@ -1,3 +1,8 @@
+# 3.4.2
+2024-09-24 (Date of Last Commit)
+
+* Added a python implementation of DoubletFinder to calculate to doublet scores in gene expression data; this does not impact the slideseq workflow
+
 # 3.4.1
 2024-09-11 (Date of Last Commit)
 

diff --git a/pipelines/skylab/slideseq/SlideSeq.wdl b/pipelines/skylab/slideseq/SlideSeq.wdl
@@ -25,7 +25,7 @@ import "../../../tasks/broad/Utilities.wdl" as utils
 
 workflow SlideSeq {
 
-    String pipeline_version = "3.4.1"
+    String pipeline_version = "3.4.2"
 
     input {
         Array[File] r1_fastq

diff --git a/...tseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md b/...tseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md
@@ -1,3 +1,7 @@
+# 2.0.1
+2024-09-24 (Date of Last Commit)
+* Added a python implementation of DoubletFinder to calculate to doublet scores in gene expression data; this does not affect the snSS2 workflow
+
 # 2.0.0
 2024-09-11 (Dat of Last Commit)
 

diff --git a/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl b/pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl
@@ -57,7 +57,7 @@ workflow MultiSampleSmartSeq2SingleNucleus {
   }
 
   # Version of this pipeline
-  String pipeline_version = "2.0.0"
+  String pipeline_version = "2.0.1"
 
   if (false) {
      String? none = "None"
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,7 +9,7 @@ import "../../../tasks/broad/Utilities.wdl" as utils @@
     workflow Multiome {
-        String pipeline_version = "5.6.1"
+        String pipeline_version = "5.7.0"
         input {
@@ Expand Down @@