Merge branch 'convert_input' into 'main'

Convert input

See merge request !1

.gitignore

@@ -3,6 +3,9 @@ workflow/images
 workflow/*.html*
 workflow/*.csv
 
+test_data/*.rds
+test_data/cxg_input.h5ad
+
 *.DS_Store
 .history
 .nextflow.log*

README.md

@@ -16,20 +16,21 @@ Hosted tutorials to learn how to use CELLxGENE are available
 
 ## Parameters
 
-Input: An h5ad file containined processed single cell RNAseq data. For
-formatting requirements, see the CELLxGENE documentation [here](https://cellxgene.cziscience.com/docs/05__Annotate%20and%20Analyze%20Your%20Data/5_3__Preparing%20Data).
+Input: An h5ad or rds file containining processed single cell RNAseq data. For
+h5ad formatting requirements, see the CELLxGENE documentation [here](https://cellxgene.cziscience.com/docs/05__Annotate%20and%20Analyze%20Your%20Data/5_3__Preparing%20Data).
+For rds files, these can contain processed Seurat or SingleCellExperiment
+objects. This workflow will attempt to convert these objects to h5ad files
+prior to loading them into CELLxGENE.
 
 ## Output
 
-This workflow does not generate any guaranteed output. Optional outputs include:
-
-- Annotations file: a CSV file containing cell labels defined by the user during
-their CELLxGENE session.
-- Marker gene lists: maybe?
+This workflow generates an interactive single cell RNA seq exploration
+interface in the browser. No output files are generated.
 
 ## Test data
 
-The test data directory contains a small test h5ad file provided by CZ CELLxGENE.
+The test data directory contains a small test h5ad file provided by CZ
+CELLxGENE as well as a script to download test data in other formats.
 
 ## Questions
 

astrocyte_pkg.yml

@@ -76,6 +76,8 @@ workflow_modules:
 # Singularity supports different registries, please specify the protocol to use.
 # Such as, "docker://", "shub://", "library://", etc. We encourage you to use the GitLab
 # container registry of BioHPC to save and manage your container images.
+workflow_containers:
+  - docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/strand-lab/cellxgene/h5ad_convert:0.0.1
 
 # A list of parameters used by the workflow, defining how to present them,
 # options etc in the web interface. For each parameter:
@@ -115,10 +117,11 @@ workflow_parameters:
   - id: input
     type: file
     required: true
-    regex: ".*h5ad$"
+    regex: "(?i).*(h5ad$|rds$)"
     description: |
-      An .h5ad file contained pre-processed single cell RNAseq data.
-      For formatting requirements, see workflow documentation.
+      An .h5ad or .rds file contained pre-processed single cell RNAseq data.
+      .h5ad files should contain an annotated AnnData object. .rds files
+      should contain an annotated Seurat or SingleCellExperiment object.
 
 # -----------------------------------------------------------------------------
 # SHINY APP CONFIGURATION
@@ -129,7 +132,7 @@ workflow_parameters:
 
 # List of any full path of the containers
 vizapp_containers:
-  - docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/strand-lab/cellxgene:latest
+  - docker://git.biohpc.swmed.edu:5050/astrocyte/workflows/strand-lab/cellxgene/cellxgene:1.2.0
 
 # List of any path of the scripts in 'your_astrocyte_workflow/vizapp' folder to run the containers
 vizapp_container_runscripts:

docs/index.md

@@ -6,12 +6,12 @@ to aid in reproducibility.
 
 ## Input
 
-To run this workflow, you must provide a pre-processed .h5ad file. The format
-requirements for this file are available [here](https://cellxgene.cziscience.com/docs/05__Annotate%20and%20Analyze%20Your%20Data/5_3__Preparing%20Data).
-
-CELLxGENE is not compatible with Seurat or SingleCellExperiment objects. These
-data types can be converted to h5ad files using the `sceasy` or `SeuratDisk`
-packages in R.
+To run this workflow, you must provide pre-processed scRNA output. This workflow
+can accept an AnnData object saved as an h5ad file (formating requirements are
+available [here](https://cellxgene.cziscience.com/docs/05__Annotate%20and%20Analyze%20Your%20Data/5_3__Preparing%20Data)),
+or an rds file containing a processed Seurat or SingleCellExperiment object. If
+an rds file is submitted, this workflow will attempt to convert it to h5ad
+using the `sceasy` R package.
 
 ## Credits
 
@@ -23,5 +23,8 @@ and at the following publication:
 > sparse matrices. CZI Single-Cell Biology, et al.
 > bioRxiv 2021.04.05; doi: https://doi.org/10.1101/2021.04.05.438318
 
+`sceasy` is an R package for the interconversion of single cell analysis formats.
+The source code is available [here](https://github.com/cellgeni/sceasy).
+
 This workflow was designed and implemented with the guidance of experts at 
 BioHPC.
\ No newline at end of file

test_data/get_test_data.R

+#!/usr/bin/env Rscript
+
+library(Seurat)
+library(SeuratData)
+library(SingleCellExperiment)
+
+pbmc <- LoadData("pbmc", type = "pbmc.final")
+pbmc_sce <- as.SingleCellExperiment(pbmc)
+
+saveRDS(pbmc, "./pbmc_seurat.rds")
+saveRDS(pbmc_sce, "./pbmc_sce.rds")
\ No newline at end of file

vizapp/run_container.sh

@@ -14,7 +14,7 @@ DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
 
 # Image settings
 REPO="cellxgene"
-TAG="latest"
+TAG="1.2.0"
 singularity_image=${REPO}-${TAG}.img
 
 outputDir=${outputDir:-"${DIR}/../workflow/output/"}

workflow/configs/biohpc.config

+// Submit jobs to SLURM scheduler
 process {
     executor = 'slurm'
     queue = 'super'
+    clusterOptions = '--hold --no-kill'
+    time = '4h'
+}
+
+// Enable singularity
+singularity {
+    enabled = true
+    cacheDir = "${projectDir}/images/singularity"
 }
 
 // Remove temporary work files
-cleanup = true
+// This will also remove logs!
+//cleanup = true
 
 // Overwrite execution report files
 // Required for nextflow version >22.10.0
-
 trace.overwrite = true
 dag.overwrite = true
 timeline.overwrite = true

workflow/main.nf

@@ -16,10 +16,11 @@
 
 params.input = "${projectDir}/../test_data/pbmc3k.h5ad"
 
-// Copy input file
+// Detect input file type and copy to h5ad
 process setup {
     stageInMode 'copy' //CxG cannot read symlinks
     publishDir "${projectDir}/output", mode: 'copy'
+    container 'git.biohpc.swmed.edu:5050/astrocyte/workflows/strand-lab/cellxgene/h5ad_convert:0.0.1'
 
     input: 
         path input
@@ -28,14 +29,30 @@ process setup {
         path "cxg_input.h5ad"
 
     script:
-        """
-        echo ""
-        echo "This script is running on:"
-        cat /etc/os-release
-        echo ""
-
-        cat $input > cxg_input.h5ad
-        """
+        // If input is h5ad, just copy it to the location
+
+        if (input.getExtension() == "h5ad") {
+            """
+            cp ${input} cxg_input.h5ad
+            """
+        }
+
+        // If input is rds, convert using the R script
+        else if (input.getExtension().toLowerCase() == "rds") {
+            """
+            source /h5ad_convert/entrypoint.sh
+            Rscript ${projectDir}/scripts/prepare_h5ad.R $input
+            """
+        }
+
+        // If neither, something's gone wrong
+        else {
+            """
+            echo "Error: Please submit either an .h5ad file, or an .rds file containing a Seurat or SingleCellExperiment object."
+            exit 1
+            """
+        }
+        
 }
 
 workflow {

workflow/scripts/prepare_h5ad.R

+# rds -> h5ad converter for CELLxGENE analysis
+# Author: John T Lafin
+
+# Load packages
+library(Seurat)
+library(sceasy)
+
+# Set up reticulate
+use_condaenv("reticulate")
+
+# Read in file
+args <- commandArgs(trailingOnly = TRUE)
+obj <- readRDS(args)
+
+# Convert Seurat object
+if (class(obj) == "Seurat") {
+    assay_name <- DefaultAssay(obj)
+
+    # If object contains a V5 assay, convert to V3
+    if (class(obj[[assay_name]]) == "Assay5") {
+        obj[["RNA3"]] <- as(obj[[assay_name]], Class = "Assay")
+        DefaultAssay(obj) <- "RNA3"
+        obj[[assay_name]] <- NULL
+        obj <- RenameAssays(obj, RNA3 = "RNA")
+    }
+
+    # Convert object to h5ad
+    convertFormat(obj, 
+    from="seurat", 
+    to="anndata",
+    outFile="cxg_input.h5ad")
+} else if (class(obj) == "SingleCellExperiment") {
+    # Convert SingleCellExperiment object
+    convertFormat(obj, 
+    from="sce", 
+    to="anndata",
+    outFile="cxg_input.h5ad")
+} else {
+    # If neither Seurat nor SCE, error
+    stop("Provided rds file does not contain a compatible Seurat or SingleCellExperiment object.")
+}
\ No newline at end of file