Upgrade Cellranger and Spaceranger (#373)

* Add support for Cellranger v7.1.0 and Spaceranger v2.0.1 * Add probe set v1.0.1 to docs * Update default versions in WDL * Update docs
lilab-bcb · Jan 29, 2023 · 417515c · 417515c
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diff --git a/docker/cellranger/7.1.0/Dockerfile b/docker/cellranger/7.1.0/Dockerfile
@@ -0,0 +1,34 @@
+FROM debian:bullseye-slim
+
+SHELL ["/bin/bash", "-c"]
+
+RUN apt-get update && \
+    apt-get install --no-install-recommends -y alien unzip rsync build-essential dpkg-dev curl gnupg procps python3 python3-pip
+
+RUN echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && \
+    curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - && \
+    apt-get update -y && apt-get install -y google-cloud-cli=415.0.0-0
+
+RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-2.9.18.zip" -o "awscliv2.zip" && \
+    unzip awscliv2.zip && \
+    ./aws/install && \
+    rm awscliv2.zip
+
+RUN ln -s /usr/bin/python3 /usr/bin/python
+
+RUN python -m pip install --upgrade pip --no-cache-dir && \
+    python -m pip install pandas==1.5.3 --no-cache-dir && \
+    python -m pip install packaging==23.0 --no-cache-dir && \
+    python -m pip install stratocumulus==0.1.7 --no-cache-dir
+
+RUN mkdir /software
+ADD https://raw.githubusercontent.com/lilab-bcb/cumulus/master/docker/monitor_script.sh /software
+ADD cellranger-7.1.0.tar.gz /software
+
+RUN apt-get -qq -y autoremove && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /var/log/dpkg.log
+
+RUN chmod a+rx /software/monitor_script.sh
+ENV PATH=/software:/software/cellranger-7.1.0:$PATH
+ENV TMPDIR=/tmp
diff --git a/docker/spaceranger/2.0.1/Dockerfile b/docker/spaceranger/2.0.1/Dockerfile
@@ -0,0 +1,33 @@
+FROM debian:bullseye-slim
+SHELL ["/bin/bash", "-c"]
+
+RUN apt-get update && \
+    apt-get install --no-install-recommends -y alien unzip build-essential dpkg-dev curl gnupg procps python3 python3-pip
+
+RUN echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && \
+    curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - && \
+    apt-get update -y && apt-get install -y google-cloud-cli=415.0.0-0
+
+RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-2.9.18.zip" -o "awscliv2.zip" && \
+    unzip awscliv2.zip && \
+    ./aws/install && \
+    rm awscliv2.zip
+
+RUN ln -s /usr/bin/python3 /usr/bin/python
+
+RUN python -m pip install --upgrade pip --no-cache-dir && \
+    python -m pip install pandas==1.5.3 --no-cache-dir && \
+    python -m pip install packaging==23.0 --no-cache-dir && \
+    python -m pip install stratocumulus==0.1.7 --no-cache-dir
+
+RUN mkdir /software
+ADD https://raw.githubusercontent.com/lilab-bcb/cumulus/master/docker/monitor_script.sh /software
+ADD spaceranger-2.0.1.tar.gz /software
+
+RUN apt-get -qq -y autoremove && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /var/log/dpkg.log
+
+RUN chmod a+rx /software/monitor_script.sh
+ENV PATH=/software:/software/spaceranger-2.0.1:$PATH
+ENV TMPDIR=/tmp
diff --git a/docs/cellranger/build_refs.rst b/docs/cellranger/build_refs.rst
@@ -94,9 +94,9 @@ We provide a wrapper of ``cellranger mkref`` to build sc/snRNA-seq references. P
 		  - Ensembl v94
 		  -
 		* - cellranger_version
-		  - cellranger version, could be: 7.0.1, 7.0.0, 6.1.2, 6.1.1
-		  - "7.0.1"
-		  - "7.0.1"
+		  - cellranger version, could be: 7.1.0, 7.0.1, 7.0.0, 6.1.2, 6.1.1
+		  - "7.1.0"
+		  - "7.1.0"
 		* - docker_registry
 		  - Docker registry to use for cellranger_workflow. Options:
 
@@ -320,9 +320,9 @@ We provide a wrapper of ``cellranger mkvdjref`` to build single-cell immune prof
 		  - Ensembl v94
 		  -
 		* - cellranger_version
-		  - cellranger version, could be: 7.0.1, 7.0.0, 6.1.2, 6.1.1
-		  - "7.0.1"
-		  - "7.0.1"
+		  - cellranger version, could be: 7.1.0, 7.0.1, 7.0.0, 6.1.2, 6.1.1
+		  - "7.1.0"
+		  - "7.1.0"
 		* - docker_registry
 		  - Docker registry to use for cellranger_workflow. Options:
 

diff --git a/docs/cellranger/feature_barcoding.rst b/docs/cellranger/feature_barcoding.rst
@@ -187,9 +187,9 @@ For feature barcoding data, ``cellranger_workflow`` takes Illumina outputs as in
 		  - 0.1
 		  - 0.1
 		* - cellranger_version
-		  - cellranger version, could be 7.0.1, 7.0.0, 6.1.2, 6.1.1, 6.0.2, 6.0.1, 6.0.0, 5.0.1, 5.0.0
-		  - "7.0.1"
-		  - "7.0.1"
+		  - cellranger version, could be: 7.1.0, 7.0.1, 7.0.0, 6.1.2, 6.1.1, 6.0.2, 6.0.1, 6.0.0, 5.0.1, 5.0.0
+		  - "7.1.0"
+		  - "7.1.0"
 		* - cumulus_feature_barcoding_version
 		  - Cumulus_feature_barcoding version for extracting feature barcode matrix. Version available: 0.11.1, 0.11.0, 0.10.0, 0.9.0, 0.8.0, 0.7.0, 0.6.0, 0.5.0, 0.4.0, 0.3.0, 0.2.0.
 		  - "0.11.1"

diff --git a/docs/cellranger/fixed_rna_profiling.rst b/docs/cellranger/fixed_rna_profiling.rst
@@ -30,12 +30,16 @@ Sample Sheet
 
         * - Keyword
           - Description
+        * - **FRP_human_probe_v1.0.1**
+          - FRP probe set v1.0.1 for human. *Only work with Cell Ranger v7.1+*.
+        * - **FRP_mouse_probe_v1.0.1**
+          - FRP probe set v1.0.1 for mouse. *Only work with Cell Ranger v7.1+*.
         * - **FRP_human_probe_v1**
-          - FRP probe set for human
+          - FRP probe set v1.0 for human. Work with Cell Ranger v7.0+.
         * - **FRP_mouse_probe_v1**
-          - FRP probe set for mouse
+          - FRP probe set v1.0 for mouse. Work with Cell Ranger v7.0+.
 
-    If *ProbeSet* column is not set, use **FRP_human_probe_v1** by default.
+    If *ProbeSet* column is not set, use **FRP_human_probe_v1.0.1** by default.
 
 #. *FeatureBarcodeFile* column.
 
@@ -136,9 +140,9 @@ For FRP data, ``cellranger_workflow`` takes Illumina outputs as input and runs `
       - false
       - false
     * - cellranger_version
-      - Cell Ranger version to use. Available versions working for FRP data: 7.0.1, 7.0.0.
-      - "7.0.1"
-      - "7.0.1"
+      - Cell Ranger version to use. Available versions working for FRP data: 7.1.0, 7.0.1, 7.0.0.
+      - "7.1.0"
+      - "7.1.0"
     * - docker_registry
       - Docker registry to use for cellranger_workflow. Options:
 

diff --git a/docs/cellranger/sc_multiomics.rst b/docs/cellranger/sc_multiomics.rst
@@ -151,9 +151,9 @@ For single-cell multiomics data, ``cellranger_workflow`` takes Illumina outputs
 	  - "gs://fc-e0000000-0000-0000-0000-000000000000/cmo_set.csv"
 	  -
 	* - cellranger_version
-	  - cellranger version, could be 7.0.1, 7.0.0, 6.1.2, 6.1.1, 6.0.2, 6.0.1, 6.0.0, 5.0.1, 5.0.0
-	  - "7.0.1"
-	  - "7.0.1"
+	  - cellranger version, could be 7.1.0, 7.0.1, 7.0.0, 6.1.2, 6.1.1, 6.0.2, 6.0.1, 6.0.0, 5.0.1, 5.0.0
+	  - "7.1.0"
+	  - "7.1.0"
 	* - cellranger_arc_version
 	  - cellranger-arc version, could be 2.0.2, 2.0.1, 2.0.0, 1.0.1, 1.0.0
 	  - "2.0.2"

diff --git a/docs/cellranger/sc_sn_rnaseq.rst b/docs/cellranger/sc_sn_rnaseq.rst
@@ -181,9 +181,9 @@ For sc/snRNA-seq data, ``cellranger_workflow`` takes Illumina outputs as input a
 		  - false
 		  - false
 		* - cellranger_version
-		  - cellranger version, could be: 7.0.1, 7.0.0, 6.1.2, 6.1.1, 6.0.2, 6.0.1, 6.0.0, 5.0.1, 5.0.0
-		  - "7.0.1"
-		  - "7.0.1"
+		  - cellranger version, could be: 7.1.0, 7.0.1, 7.0.0, 6.1.2, 6.1.1, 6.0.2, 6.0.1, 6.0.0, 5.0.1, 5.0.0
+		  - "7.1.0"
+		  - "7.1.0"
 		* - config_version
 		  - config docker version used for processing sample sheets, could be 0.3, 0.2, 0.1
 		  - "0.3"

diff --git a/docs/cellranger/sc_vdj.rst b/docs/cellranger/sc_vdj.rst
@@ -123,9 +123,9 @@ For scIR-seq data, ``cellranger_workflow`` takes Illumina outputs as input and r
 	  - "auto"
 	  - "auto"
 	* - cellranger_version
-	  - cellranger version, could be 7.0.1, 7.0.0, 6.1.2, 6.1.1, 6.0.2, 6.0.1, 6.0.0, 5.0.1, 5.0.0
-	  - "7.0.1"
-	  - "7.0.1"
+	  - cellranger version, could be 7.1.0, 7.0.1, 7.0.0, 6.1.2, 6.1.1, 6.0.2, 6.0.1, 6.0.0, 5.0.1, 5.0.0
+	  - "7.1.0"
+	  - "7.1.0"
 	* - docker_registry
 	  - Docker registry to use for cellranger_workflow. Options:
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -5,7 +5,7 @@
 Release Highlights in Current Stable
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. include:: release_notes/version_2_3.rst
+.. include:: release_notes/version_2_4.rst
 
 .. toctree::
    :maxdepth: 1

diff --git a/docs/release_notes.rst b/docs/release_notes.rst
@@ -3,6 +3,11 @@ Release notes
 
 .. role:: small
 
+Version 2.4
+~~~~~~~~~~~~~~
+
+.. include:: release_notes/version_2_4.rst
+
 Version 2.3
 ~~~~~~~~~~~~~~
 

diff --git a/docs/release_notes/version_2_4.rst b/docs/release_notes/version_2_4.rst
@@ -0,0 +1,20 @@
+2.4.0 :small:`January 28, 2023`
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+**Updates:**
+
+* In Cellranger workflow:
+
+    * Upgrade *cellranger_version* default to ``7.1.0``.
+    * Add Mouse probe set v1.0 for `Fixed RNA Profiling`_ analysis.
+    * Add probe set v1.0.1 of both Human and Mouse for `Fixed RNA Profiling`_ analysis.
+    * Upgrade *cumulus_feature_barcoding* version default to ``0.11.1``.
+
+* In Cellranger_create_reference workflow: upgrade *cellranger_version* default to ``7.1.0``.
+
+* In Cellranger_vdj_create_reference workflow: upgrade *cellranger_version* default to ``7.1.0``.
+
+* In Spaceranger workflow: upgrade *spaceranger_version* default to ``2.0.1``.
+
+
+.. _Fixed RNA Profiling: ./cellranger/index.html#fixed-rna-profiling
diff --git a/docs/spaceranger.rst b/docs/spaceranger.rst
@@ -265,9 +265,9 @@ For spatial data, ``spaceranger_workflow`` takes Illumina outputs and related im
 		  - 50
 		  -
 		* - spaceranger_version
-		  - spaceranger version, could be: ``2.0.0``, ``1.3.1``, ``1.3.0``
-		  - "2.0.0"
-		  - "2.0.0"
+		  - spaceranger version, could be: 2.0.1, 2.0.0, 1.3.1, 1.3.0
+		  - "2.0.1"
+		  - "2.0.1"
 		* - config_version
 		  - config docker version used for processing sample sheets, could be 0.3.
 		  - "0.3"

diff --git a/workflows/cellranger/cellranger_create_reference.wdl b/workflows/cellranger/cellranger_create_reference.wdl
@@ -22,8 +22,8 @@ workflow cellranger_create_reference {
 
         # Which docker registry to use
         String docker_registry = "quay.io/cumulus"
-        # 7.0.1, 7.0.0, 6.1.2, 6.1.1
-        String cellranger_version = "7.0.1"
+        # 7.1.0, 7.0.1, 7.0.0, 6.1.2, 6.1.1
+        String cellranger_version = "7.1.0"
 
         # Disk space in GB
         Int disk_space = 100

diff --git a/workflows/cellranger/cellranger_vdj_create_reference.wdl b/workflows/cellranger/cellranger_vdj_create_reference.wdl
@@ -16,8 +16,8 @@ workflow cellranger_vdj_create_reference {
 
         # Which docker registry to use
         String docker_registry = "quay.io/cumulus"
-        # 7.0.1, 7.0.0, 6.1.2, 6.1.1
-        String cellranger_version = "7.0.1"
+        # 7.1.0, 7.0.1, 7.0.0, 6.1.2, 6.1.1
+        String cellranger_version = "7.1.0"
 
         # Disk space in GB
         Int disk_space = 100

diff --git a/workflows/cellranger/cellranger_workflow.wdl b/workflows/cellranger/cellranger_workflow.wdl
@@ -98,8 +98,8 @@ workflow cellranger_workflow {
         # Index TSV file
         File acronym_file = "gs://regev-lab/resources/cellranger/index.tsv"
 
-        # 7.0.1, 7.0.0, 6.1.2, 6.1.1, 6.0.2, 6.0.1, 6.0.0, 5.0.1, 5.0.0
-        String cellranger_version = "7.0.1"
+        # 7.1.0, 7.0.1, 7.0.0, 6.1.2, 6.1.1, 6.0.2, 6.0.1, 6.0.0, 5.0.1, 5.0.0
+        String cellranger_version = "7.1.0"
         # 0.11.1, 0.11.0, 0.10.0, 0.9.0, 0.8.0, 0.7.0, 0.6.0, 0.5.0, 0.4.0, 0.3.0, 0.2.0
         String cumulus_feature_barcoding_version = "0.11.1"
         # 2.1.0, 2.0.0, 1.2.0, 1.1.0

diff --git a/workflows/cellranger/index.tsv b/workflows/cellranger/index.tsv
@@ -57,7 +57,9 @@ human_probe_v1	gs://regev-lab/resources/cellranger/Visium_Human_Transcriptome_Pr
 human_probe_v2	gs://regev-lab/resources/cellranger/Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A.csv
 mouse_probe_v1	gs://regev-lab/resources/cellranger/Visium_Mouse_Transcriptome_Probe_Set_v1.0_mm10-2020-A.csv
 FRP_human_probe_v1	gs://regev-lab/resources/cellranger/Chromium_Human_Transcriptome_Probe_Set_v1.0_GRCh38-2020-A.csv
+FRP_human_probe_v1.0.1	gs://regev-lab/resources/cellranger/Chromium_Human_Transcriptome_Probe_Set_v1.0.1_GRCh38-2020-A.csv
 FRP_mouse_probe_v1	gs://regev-lab/resources/cellranger/Chromium_Mouse_Transcriptome_Probe_Set_v1.0_mm10-2020-A.csv
+FRP_mouse_probe_v1.0.1	gs://regev-lab/resources/cellranger/Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1_mm10-2020-A.csv
 SC3Pv3	gs://regev-lab/resources/cellranger/3M-february-2018.txt.gz
 SC3Pv2	gs://regev-lab/resources/cellranger/737K-august-2016.txt.gz
 fiveprime	gs://regev-lab/resources/cellranger/737K-august-2016.txt.gz

diff --git a/workflows/spaceranger/spaceranger_workflow.wdl b/workflows/spaceranger/spaceranger_workflow.wdl
@@ -47,8 +47,8 @@ workflow spaceranger_workflow {
         # Hard trim the input Read 2 to this length before analysis
         Int? r2_length
 
-        # Space Ranger version: 2.0.0, 1.3.1, 1.3.0
-        String spaceranger_version = "2.0.0"
+        # Space Ranger version: 2.0.1, 2.0.0, 1.3.1, 1.3.0
+        String spaceranger_version = "2.0.1"
         # Config version
         String config_version = "0.3"