Add Fixed RNA Profiling to Cellranger workflow (#365)

* update index * update cellranger_multi with Fixed RNA Profiling * upgrade default cellranger versions in cellranger WDLs * update docs
lilab-bcb · Oct 31, 2022 · 88cd9c9 · 88cd9c9
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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: ``7.0.0``, ``6.1.2``, ``6.1.1``
-		  - "7.0.0"
-		  - "7.0.0"
+		  - cellranger version, could be: 7.0.1, 7.0.0, 6.1.2, 6.1.1
+		  - "7.0.1"
+		  - "7.0.1"
 		* - 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: 7.0.0, 6.1.2, 6.1.1
-		  - "7.0.0"
-		  - "7.0.0"
+		  - cellranger version, could be: 7.0.1, 7.0.0, 6.1.2, 6.1.1
+		  - "7.0.1"
+		  - "7.0.1"
 		* - 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 7.0.0, 6.1.2, 6.1.1, 6.0.2, 6.0.1, 6.0.0, 5.0.1, 5.0.0
-		  - "7.0.0"
-		  - "7.0.0"
+		  - 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"
 		* - cumulus_feature_barcoding_version
 		  - Cumulus_feature_barcoding version for extracting feature barcode matrix. Version available: 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.
 		  - "0.11.0"

diff --git a/docs/cellranger/fixed_rna_profiling.rst b/docs/cellranger/fixed_rna_profiling.rst
@@ -0,0 +1,214 @@
+Cellranger multi supports `Fixed RNA Profiling`_ since version 7.0.0.
+
+Sample Sheet
+++++++++++++++
+
+#. **Reference** column.
+
+    Prebuilt scRNA-seq references for FRP data processing are summarized below.
+
+    .. list-table::
+        :widths: 5 20
+        :header-rows: 1
+
+        * - Keyword
+          - Description
+        * - **GRCh38-2020-A**
+          - Human GRCh38 (GENCODE v32/Ensembl 98)
+
+#. *DataType* column.
+
+    Set ``frp`` for RNA-Seq modalities of your FRP samples. For other modalities (e.g. citeseq or antibody), set to their corresponding data types.
+
+#. *ProbeSet* column.
+
+    Preset probe set references for FRP samples:
+
+    .. list-table::
+        :widths: 5 20
+        :header-rows: 1
+
+        * - Keyword
+          - Description
+        * - **FRP_human_probe_v1**
+          - FRP probe set for human
+
+    If *ProbeSet* column is not set, use **FRP_human_probe_v1** by default.
+
+#. *FeatureBarcodeFile* column.
+
+    Provide sample name - Probe Barcode association as follows::
+
+        sample1,BC001|BC002,Control
+        sample2,BC003|BC004,Treated
+
+    where the third column (i.e. ``Control`` and ``Treated`` above) is optional, which specifies the description of the samples.
+
+#. *Link* column.
+
+    Put a sample unique link name for all modalities that are linked.
+
+    If *Link* column is not set, only consider RNA-seq modalities (i.e. samples of *DataType* ``frp``) and use their *Sample* names as the *Link* names.
+
+#. Example::
+
+    Sample,Reference,ProbeSet,Flowcell,DataType,FeatureBarcodeFile,Link
+    sample1,GRCh38-2020-A,FRP_human_probe_v1,/path/to/sample1/fastq/folder,frp,/path/to/sample1/fbf/file,
+    sample2_rna,GRCh38-2020-A,FRP_human_probe_v1,/path/to/sample2/rna/fastq/folder,frp,/path/to/sample2/rna/fbf/file,sample2
+    sample2_citeseq,GRCh38-2020-A,,/path/to/sample2/citeseq/fastq/folder,citeseq,/path/to/sample2/citeseq/fbf/file,sample2
+
+In the example above, two linked samples are provided.
+
+
+Workflow Input
+++++++++++++++++
+
+For FRP data, ``cellranger_workflow`` takes Illumina outputs as input and runs ``cellranger mkfastq`` and ``cellranger multi``. Revalant workflow inputs are described below, with required inputs highlighted in **bold**:
+
+.. list-table::
+    :widths: 5 30 30 20
+    :header-rows: 1
+
+    * - Name
+      - Description
+      - Example
+      - Default
+    * - **input_csv_file**
+      - Sample Sheet (contains Sample, Reference, DataType, Flowcell as required; Lane and Index are required if *run_mkfastq* is ``true``; ProbeSet, FeatureBarcodeFile and Link are optional)
+      - "gs://fc-e0000000-0000-0000-0000-000000000000/sample_sheet.csv"
+      -
+    * - **output_directory**
+      - Output directory
+      - "gs://fc-e0000000-0000-0000-0000-000000000000/cellranger_output"
+      -
+    * - run_mkfastq
+      - If you want to run ``cellranger mkfastq``
+      - true
+      - true
+    * - run_count
+      - If you want to run ``cellranger multi``
+      - true
+      - true
+    * - delete_input_bcl_directory
+      - If delete BCL directories after demux. If false, you should delete this folder yourself so as to not incur storage charges
+      - false
+      - false
+    * - mkfastq_barcode_mismatches
+      - Number of mismatches allowed in matching barcode indices (bcl2fastq2 default is 1)
+      - 0
+      - 1
+    * - mkfastq_force_single_index
+      - If 10x-supplied i7/i5 paired indices are specified, but the flowcell was run with only one sample index, allow the demultiplex to proceed using the i7 half of the sample index pair
+      - false
+      - false
+    * - mkfastq_filter_single_index
+      - Only demultiplex samples identified by an i7-only sample index, ignoring dual-indexed samples. Dual-indexed samples will not be demultiplexed
+      - false
+      - false
+    * - mkfastq_use_bases_mask
+      - Override the read lengths as specified in RunInfo.xml
+      - "“Y28n*,I8n*,N10,Y90n*”"
+      -
+    * - mkfastq_delete_undetermined
+      - Delete undetermined FASTQ files generated by bcl2fastq2
+      - false
+      - false
+    * - force_cells
+      - Force pipeline to use this number of cells, bypassing the cell detection algorithm, mutually exclusive with expect_cells. This option is used by ``cellranger multi``.
+      - 6000
+      -
+    * - expect_cells
+      - Expected number of recovered cells. Mutually exclusive with force_cells. This option is used by ``cellranger multi``.
+      - 3000
+      -
+    * - include_introns
+      - Turn this option on to also count reads mapping to intronic regions. With this option, users do not need to use pre-mRNA references. Note that if this option is set, cellranger_version must be >= 5.0.0. This option is used by ``cellranger multi``.
+      - true
+      - true
+    * - no_bam
+      - Turn this option on to disable BAM file generation. This option is only available if cellranger_version >= 5.0.0. This option is used by ``cellranger multi``.
+      - false
+      - false
+    * - secondary
+      - Perform Cell Ranger secondary analysis (dimensionality reduction, clustering, etc.). This option is used by ``cellranger multi``.
+      - 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"
+    * - docker_registry
+      - Docker registry to use for cellranger_workflow. Options:
+
+        - "quay.io/cumulus" for images on Red Hat registry;
+
+        - "cumulusprod" for backup images on Docker Hub.
+      - "quay.io/cumulus"
+      - "quay.io/cumulus"
+    * - mkfastq_docker_registry
+      - Docker registry to use for ``cellranger mkfastq``. Default is the registry to which only Broad users have access. See :ref:`bcl2fastq-docker` for making your own registry.
+      - "gcr.io/broad-cumulus"
+      - "gcr.io/broad-cumulus"
+    * - acronym_file
+      - | The link/path of an index file in TSV format for fetching preset genome references, probe set references, chemistry whitelists, etc. by their names.
+        | Set an GS URI if *backend* is ``gcp``; an S3 URI for ``aws`` backend; an absolute file path for ``local`` backend.
+      - "s3://xxxx/index.tsv"
+      - "gs://regev-lab/resources/cellranger/index.tsv"
+    * - zones
+      - Google cloud zones
+      - "us-central1-a us-west1-a"
+      - "us-central1-a us-central1-b us-central1-c us-central1-f us-east1-b us-east1-c us-east1-d us-west1-a us-west1-b us-west1-c"
+    * - num_cpu
+      - Number of cpus to request for one node for cellranger mkfastq and cellranger multi
+      - 32
+      - 32
+    * - memory
+      - Memory size string for cellranger mkfastq and cellranger multi
+      - "120G"
+      - "120G"
+    * - mkfastq_disk_space
+      - Optional disk space in GB for mkfastq
+      - 1500
+      - 1500
+    * - count_disk_space
+      - Disk space in GB needed for cellranger multi
+      - 500
+      - 500
+    * - backend
+      - Cloud backend for file transfer and computation. Available options:
+
+        - "gcp" for Google Cloud;
+        - "aws" for Amazon AWS;
+        - "local" for local machines.
+      - "gcp"
+      - "gcp"
+    * - preemptible
+      - Number of preemptible tries
+      - 2
+      - 2
+    * - awsQueueArn
+      - The AWS ARN string of the job queue to be used. This only works for ``aws`` backend.
+      - "arn:aws:batch:us-east-1:xxx:job-queue/priority-gwf"
+      - ""
+
+Workflow Output
++++++++++++++++++
+
+See the table below for important outputs:
+
+.. list-table::
+    :widths: 5 5 10
+    :header-rows: 1
+
+    * - Name
+      - Type
+      - Description
+    * - fastq_outputs
+      - Array[Array[String]]
+      - ``fastq_outputs[0]`` gives the list of cloud urls containing FASTQ files for RNA-Seq modalities of FRP data, one url per flowcell.
+    * - count_outputs
+      - Map[String, Array[String]]
+      - ``count_outputs["multi"]`` gives the list of cloud urls containing *cellranger multi* outputs, one url per sample.
+
+
+.. _Fixed RNA Profiling: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/multi-frp
diff --git a/docs/cellranger/general_steps.rst b/docs/cellranger/general_steps.rst
@@ -85,7 +85,10 @@ Alternatively, users can submit jobs through command line interface (CLI) using
 			| **cmo** refers to cell multiplexing oligos used in 10x Genomics' CellPlex assay,
 			| **crispr** refers to Perturb-seq guide tag data,
 			| **atac** refers to scATAC-Seq data (*cellranger-atac count*),
+			| **frp** refers to Fixed RNA Profiling (FRP) gene expression data,
 			| This column is optional and the default data type is *rna*.
+		* - ProbeSet
+		  - Probe set reference for FRP samples. Currently ``FRP_human_probe_v1`` is the only available and thus the default reference. Only works for samples of *DataType* ``frp``.
 		* - FeatureBarcodeFile
 		  -
 		  	| Google bucket urls pointing to feature barcode files for *rna*, *citeseq*, *hashing*, *cmo* and *crispr* data.
@@ -94,7 +97,7 @@ Alternatively, users can submit jobs through command line interface (CLI) using
 		  	| This column is only required for targeted gene expression analysis (*rna*), CITE-Seq (*citeseq*), cell-hashing or nucleus-hashing (*hashing*), CellPlex (*cmo*) and Perturb-seq (*crispr*).
 		* - Link
 		  -
-			| Designed for Single Cell Multiome	ATAC + Gene Expression, Feature Barcoding, or CellPlex.
+			| Designed for Single Cell Multiome	ATAC + Gene Expression, Feature Barcoding, CellPlex, or FRP.
 			| Link multiple modalities together using a single link name.
 			| cellranger-arc count, cellranger count, or cellranger multi will be triggered automatically depending on the modalities.
 			| If empty string is provided, no link is assumed.

diff --git a/docs/cellranger/index.rst b/docs/cellranger/index.rst
@@ -43,6 +43,13 @@ Single-cell multiomics
 
 .. include:: sc_multiomics.rst
 
+--------------------------
+
+Fixed RNA Profiling
+^^^^^^^^^^^^^^^^^^^^
+
+.. include:: fixed_rna_profiling.rst
+
 ---------------------------------
 
 Build Cell Ranger References

diff --git a/docs/cellranger/sc_multiomics.rst b/docs/cellranger/sc_multiomics.rst
@@ -151,13 +151,13 @@ 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 7.0.0, 6.1.2, 6.1.1, 6.0.2, 6.0.1, 6.0.0, 5.0.1, 5.0.0
-	  - "7.0.0"
-	  - "7.0.0"
+	  - 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_arc_version
-	  - cellranger-arc version, could be 2.0.1, 2.0.0, 1.0.1, 1.0.0
-	  - "2.0.1"
-	  - "2.0.1"
+	  - cellranger-arc version, could be 2.0.2, 2.0.1, 2.0.0, 1.0.1, 1.0.0
+	  - "2.0.2"
+	  - "2.0.2"
 	* - docker_registry
 	  - Docker registry to use for cellranger_workflow. Options:
 

diff --git a/docs/cellranger/sc_sn_rnaseq.rst b/docs/cellranger/sc_sn_rnaseq.rst
@@ -181,13 +181,13 @@ For sc/snRNA-seq data, ``cellranger_workflow`` takes Illumina outputs as input a
 		  - false
 		  - false
 		* - cellranger_version
-		  - cellranger version, could be: 7.0.0, 6.1.2, 6.1.1, 6.0.2, 6.0.1, 6.0.0, 5.0.1, 5.0.0
-		  - "7.0.0"
-		  - "7.0.0"
+		  - 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"
 		* - config_version
-		  - config docker version used for processing sample sheets, could be 0.2, 0.1
-		  - "0.2"
-		  - "0.2"
+		  - config docker version used for processing sample sheets, could be 0.3, 0.2, 0.1
+		  - "0.3"
+		  - "0.3"
 		* - docker_registry
 		  - Docker registry to use for cellranger_workflow. Options:
 

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 7.0.0, 6.1.2, 6.1.1, 6.0.2, 6.0.1, 6.0.0, 5.0.1, 5.0.0
-	  - "7.0.0"
-	  - "7.0.0"
+	  - 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"
 	* - docker_registry
 	  - Docker registry to use for cellranger_workflow. Options:
 

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"
-        # 7.0.0, 6.1.2, 6.1.1
-        String cellranger_version = "7.0.0"
+        # 7.0.1, 7.0.0, 6.1.2, 6.1.1
+        String cellranger_version = "7.0.1"
 
         # Disk space in GB
         Int disk_space = 100