Add ArchR. Upgrade to Cell Ranger ATAC v2.1.0

hisplan · Apr 15, 2022 · 14f146f · 14f146f
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Showing 3 changed files with 36 additions and 12 deletions.
diff --git a/README.md b/README.md
@@ -23,17 +23,17 @@ FastQC            | A high throughput sequence QC analysis tool              | 0
 Transgenes        | Creating a reference package with transgenes             | 0.0.8
 Cell Ranger GEX   | Single-cell gene expression (3' and 5')                  | 6.1.2
 Cell Ranger V(D)J | Single-cell immune profiling (TCR/BCR)                   | 6.1.2
-Cell Ranger ATAC  | Single-cell chromatin accessbility (ATAC)                | 2.0.0
+Cell Ranger ATAC  | Single-cell chromatin accessbility (ATAC)                | 2.1.0
 Cell Ranger ARC   | Single-cell multiome ATAC + Gene Expression              | 2.0.0
 Space Ranger      | Single-cell spatial gene expression                      | 1.3.1
 CellPlex          | Cell multiplexing                                        | 6.1.2
 mkref             | Creating a human+mouse hybrid genome                     | 0.0.6
+ArchR             | Processing and analyzing single-cell ATAC-seq data       | 0.1.0
 
 Coming Soon
 
 Pipeline          | Description
 ----------------- | --------------------------------------------------------------
-ArchR             | Processing and analyzing single-cell ATAC-seq data
 Mito Tracing      | Lineage tracing using mitochondrial mutations
 
 ## Prerequisites

diff --git a/config.dev.yaml b/config.dev.yaml
@@ -89,7 +89,7 @@ containers:
     - name: fai2gtf
       version: 0.2.0
       project_url: https://github.com/hisplan/wdl-transgenes
-      download_url: https://github.com/hisplan/wdl-transgenes/archive/refs/tags/v0.0.7.tar.gz
+      download_url: https://github.com/hisplan/wdl-transgenes/archive/refs/tags/v0.0.8.tar.gz
       directory: dockers/fai2gtf
     - name: gtf-utils
       version: 0.0.6
@@ -104,13 +104,21 @@ containers:
       project_url: https://github.com/hisplan/docker-cellranger-arc
       download_url: https://github.com/hisplan/docker-cellranger-arc/archive/refs/tags/v2.0.0.tar.gz
     - name: cellranger-atac
-      version: 2.0.0
+      version: 2.1.0
       project_url: https://github.com/hisplan/docker-cellranger-atac
-      download_url: https://github.com/hisplan/docker-cellranger-atac/archive/refs/tags/v2.0.0.tar.gz
+      download_url: https://github.com/hisplan/docker-cellranger-atac/archive/refs/tags/v2.1.0.tar.gz
     - name: spaceranger
       version: 1.3.1
       project_url: https://github.com/hisplan/docker-spaceranger
       download_url: https://github.com/hisplan/docker-spaceranger/archive/refs/tags/v1.3.1.tar.gz
+    - name: archr
+      version: 0.9.x-snapshot-20200922b
+      project_url: https://github.com/hisplan/docker-archr
+      download_url: https://github.com/hisplan/docker-archr/archive/refs/tags/v0.9.x-snapshot-20200922b.tar.gz
+    - name: archr2adata
+      version: 0.0.3
+      project_url: https://github.com/hisplan/archr2adata
+      download_url: https://github.com/hisplan/archr2adata/archive/refs/tags/v0.0.3.tar.gz
 
 pipelines:
   packages:
@@ -155,9 +163,9 @@ pipelines:
       project_url: https://github.com/hisplan/wdl-cellranger-arc
       download_url: https://github.com/hisplan/wdl-cellranger-arc/archive/refs/tags/v2.0.0.tar.gz
     - name: cellranger-atac
-      version: 2.0.0
+      version: 2.1.0
       project_url: https://github.com/hisplan/wdl-cellranger-atac
-      download_url: https://github.com/hisplan/wdl-cellranger-atac/archive/refs/tags/v2.0.0.tar.gz
+      download_url: https://github.com/hisplan/wdl-cellranger-atac/archive/refs/tags/v2.1.0.tar.gz
     - name: spaceranger
       version: 1.3.1
       project_url: https://github.com/hisplan/wdl-spaceranger
@@ -166,3 +174,7 @@ pipelines:
       version: 0.0.6
       project_url: https://github.com/hisplan/wdl-mkref
       download_url: https://github.com/hisplan/wdl-mkref/archive/refs/tags/v0.0.6.tar.gz
+    - name: archr
+      version: 0.1.0
+      project_url: https://github.com/hisplan/wdl-ArchR
+      download_url: https://github.com/hisplan/wdl-ArchR/archive/refs/tags/v0.1.0.tar.gz
diff --git a/config.yaml b/config.yaml
@@ -72,7 +72,7 @@ containers:
       version: 0.2.0
       project_url: https://github.com/hisplan/sharp/tree/master/dockers/basic-qc
       download_url: https://github.com/hisplan/sharp/archive/refs/tags/v0.1.0.tar.gz
-      directory: dockers/cut-indrop-spacer      
+      directory: dockers/cut-indrop-spacer
     - name: cite-seq-count
       version: 1.4.2-develop
       project_url: https://github.com/hisplan/sharp/tree/master/dockers/cite-seq-count
@@ -104,13 +104,21 @@ containers:
       project_url: https://github.com/hisplan/docker-cellranger-arc
       download_url: https://github.com/hisplan/docker-cellranger-arc/archive/refs/tags/v2.0.0.tar.gz
     - name: cellranger-atac
-      version: 2.0.0
+      version: 2.1.0
       project_url: https://github.com/hisplan/docker-cellranger-atac
-      download_url: https://github.com/hisplan/docker-cellranger-atac/archive/refs/tags/v2.0.0.tar.gz
+      download_url: https://github.com/hisplan/docker-cellranger-atac/archive/refs/tags/v2.1.0.tar.gz
     - name: spaceranger
       version: 1.3.1
       project_url: https://github.com/hisplan/docker-spaceranger
       download_url: https://github.com/hisplan/docker-spaceranger/archive/refs/tags/v1.3.1.tar.gz
+    - name: archr
+      version: 0.9.x-snapshot-20200922b
+      project_url: https://github.com/hisplan/docker-archr
+      download_url: https://github.com/hisplan/docker-archr/archive/refs/tags/v0.9.x-snapshot-20200922b.tar.gz
+    - name: archr2adata
+      version: 0.0.3
+      project_url: https://github.com/hisplan/archr2adata
+      download_url: https://github.com/hisplan/archr2adata/archive/refs/tags/v0.0.3.tar.gz
 
 pipelines:
   packages:
@@ -155,9 +163,9 @@ pipelines:
       project_url: https://github.com/hisplan/wdl-cellranger-arc
       download_url: https://github.com/hisplan/wdl-cellranger-arc/archive/refs/tags/v2.0.0.tar.gz
     - name: cellranger-atac
-      version: 2.0.0
+      version: 2.1.0
       project_url: https://github.com/hisplan/wdl-cellranger-atac
-      download_url: https://github.com/hisplan/wdl-cellranger-atac/archive/refs/tags/v2.0.0.tar.gz
+      download_url: https://github.com/hisplan/wdl-cellranger-atac/archive/refs/tags/v2.1.0.tar.gz
     - name: spaceranger
       version: 1.3.1
       project_url: https://github.com/hisplan/wdl-spaceranger
@@ -166,3 +174,7 @@ pipelines:
       version: 0.0.6
       project_url: https://github.com/hisplan/wdl-mkref
       download_url: https://github.com/hisplan/wdl-mkref/archive/refs/tags/v0.0.6.tar.gz
+    - name: archr
+      version: 0.1.0
+      project_url: https://github.com/hisplan/wdl-ArchR
+      download_url: https://github.com/hisplan/wdl-ArchR/archive/refs/tags/v0.1.0.tar.gz