Merge branch 'develop' into 'master'

Develop See merge request !57

Merge branch 'develop' into 'master'
Develop See merge request !57
caecad18 · Gervaise Henry · 4b102a5e · bedc0841 · caecad18 · caecad18
Commit caecad18 authored 5 years ago by Gervaise Henry
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -36,16 +36,19 @@ simple_1:
    - branches
    - tags
  except:
-    - develop
+    refs:
-    - master
+      - develop
+      - master
  script:
-  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2'
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.1.0'
-  - pytest -m count302
+  - pytest -m count310
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
    paths:
      - .nextflow.log
+      - workflow/output/count310/sample1/outs/web_summary.html
+      - workflow/output/multiqc/run/multiqc_report.html
    expire_in: 2 days
  retry:
    max: 1
@@ -57,17 +60,20 @@ simple_2:
  only:
    - branches
  except:
-    - develop
+    refs:
-    - master
+      - develop
-    - tags
+      - master
+      - tags
  script:
-  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v3s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.1'
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v3s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.1.0'
-  - pytest -m count301
+  - pytest -m count310
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
    paths:
      - .nextflow.log
+      - workflow/output/count310/sample1/outs/web_summary.html
+      - workflow/output/multiqc/run/multiqc_report.html
    expire_in: 2 days
  retry:
    max: 1
@@ -80,36 +86,43 @@ detailed_1:
    - develop
    - master
  except:
-    - tags
+    refs:
+      - tags
  script:
-  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.1.0'
-  - pytest -m count302
+  - pytest -m count310
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
    paths:
      - .nextflow.log
+      - workflow/output/count310/sample1/outs/web_summary.html
+      - workflow/output/multiqc/run/multiqc_report.html
    expire_in: 2 days
  retry:
    max: 1
    when:
      - always
 detailed_2:
  stage: detailed
  only:
    - develop
    - master
  except:
-    - tags
+    refs:
+      - tags
  script:
-  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v3s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v3s2r10k/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.2'
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
  - pytest -m count302
  artifacts:
    name: "$CI_JOB_NAME"
    when: always
    paths:
      - .nextflow.log
+      - workflow/output/count302/sample1/outs/web_summary.html
+      - workflow/output/multiqc/run/multiqc_report.html
    expire_in: 2 days
  retry:
    max: 1
@@ -122,7 +135,32 @@ detailed_3:
    - develop
    - master
  except:
-    - tags
+    refs:
+      - tags
+  script:
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v3s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v3s2r10k/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.1'
+  - pytest -m count301
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - .nextflow.log
+      - workflow/output/count301/sample1/outs/web_summary.html
+      - workflow/output/multiqc/run/multiqc_report.html
+    expire_in: 2 days
+  retry:
+    max: 1
+    when:
+      - always
+detailed_4:
+  stage: detailed
+  only:
+    - develop
+    - master
+  except:
+    refs:
+      - tags
  script:
  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v2s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
  - pytest -m count211
@@ -131,6 +169,8 @@ detailed_3:
    when: always
    paths:
      - .nextflow.log
+      - workflow/output/count211/sample1/outs/web_summary.html
+      - workflow/output/multiqc/run/multiqc_report.html
    expire_in: 2 days
  retry:
    max: 1

--- a/CHANGELOG.md
+++ b/CHANGELOG.md
-# v1.1.0 (in development)
+# v1.2.0
+**User Facing**
+* Add Cellranger Version 3.1.0
+* Add human/mouse farmyard reference Version 3.1.0 from 10x
+* Add Vizapp (shiny)
+* Fix mutiqc error
+* Add MIT License
+**Background**
+* Add CI Artifacts
+*Known Bugs*
+* Vizapp does not yet work for Astrocyte
+# v1.1.0
 **User Facing**
 * Make report (multiqc) for cellranger qc output, version, references

--- a/LICENSE
+++ b/LICENSE
+MIT License
+Copyright (c) 2019 University of Texas Southwestern Medical Center.
+Contributors: Gervaise H. Henry, Jeremy Mathews, and Venkat Malladi
+Department: Bioinformatic Core Facility, Department of Bioinformatics
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
--- a/README.md
+++ b/README.md
@@ -27,7 +27,7 @@ To Run:
    * path to the fastq location
    * R1 and R2 only necessary but can include I2
    * only fastq's in designFile (see below) are used, not present will be ignored
-    * eg: **--fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/\*.fastq.gz'**
+    * eg: **--fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/\*.fastq.gz'**
  * **--designFile**
    * path to design file (csv format) location
    * column 1 = "Sample"
@@ -35,7 +35,7 @@ To Run:
    * column 3 = "fastq_R2"
    * can have repeated "Sample" if there are multiple fastq R1/R2 pairs for the samples
    * can be downloaded [HERE](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/master/docs/design.csv)
-    * eg: **--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/design.csv'**
+    * eg: **--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/design.csv'**
  * **--genome**
    * reference genome
    * requires workflow/conf/biohpc.config to work
@@ -46,8 +46,9 @@ To Run:
        * *'hg19-1.2.0'* = Human GRCh37 (hg19) release 84
        * *'mm10-3.0.0'* = Mouse GRCm38 (mm10) release 93
        * *'mm10-3.0.0'* = Mouse GRCm38 (mm10) release 84
-        * *'hg19_and_mm10-3.0.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 93
+        * *'GRCh38_and_mm10-3.1.0'* = Human GRCh38 + Mouse GRCm38 (mm10) release 93
-        * *'hg19_and_mm10-1.2.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84
+        * *'hg19_and_mm10-3.0.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm10) release 93
+        * *'hg19_and_mm10-1.2.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm10) release 84
        * *'ercc92-1.2.0'* = ERCC.92 Spike-In
    * if --genome is used then --genomeLocationFull is not necessary
    * eg: **--genome 'GRCh38-3.0.0'**
@@ -83,16 +84,17 @@ To Run:
    * cellranger version
    * --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
    * options:
+        * *'3.1.0'*
        * *'3.0.2'*
        * *'3.0.1'*
        * *'2.1.1'*
-    * eg: **--version '3.0.2'**
+    * eg: **--version '3.1.0'**
  * **--outDir**
    * optional output directory for run
    * eg: **--outDir 'test'**
 * FULL EXAMPLE:
  ```
-  nextflow run workflow/main.nf --fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/*.fastq.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r100k/design.csv' --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2' --outDir 'test'
+  nextflow run workflow/main.nf --fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/*.fastq.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/design.csv' --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.1.0' --outDir 'test'
  ```
 * Design example:

--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -43,6 +43,7 @@ workflow_modules:
  - 'cellranger/2.1.1'
  - 'cellranger/3.0.1'
  - 'cellranger/3.0.2'
+  - 'cellranger/3.1.0'
  - 'bcl2fastq/2.17.1.14'
  - 'multiqc/1.7'
@@ -104,8 +105,9 @@ workflow_parameters:
      - ['hg19-1.2.0', 'Human GRCh37 (hg19) release 84']
      - ['mm10-3.0.0', 'Mouse GRCm38 (mm10) release 93']
      - ['mm10-1.2.0', 'Mouse GRCm38 (mm10) release 84']
-      - ['hg19_and_mm10-3.0.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 93']
+      - ['GRCh38_and_mm10-3.1.0', 'Human GRCh38 + Mouse GRCm38 (mm10) release 93']
-      - ['hg19_and_mm10-1.2.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84']
+      - ['hg19_and_mm10-3.0.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm10) release 93']
+      - ['hg19_and_mm10-1.2.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm10) release 84']
      - ['ercc92-1.2.0', 'ERCC.92 Spike-In']
    required: true
    description: |
@@ -142,8 +144,9 @@ workflow_parameters:
  - id: version
    type: select
-    default: '3.0.2'
+    default: '3.1.0'
    choices:
+      - ['3.1.0', '3.1.0']
      - ['3.0.2', '3.0.2']
      - ['3.0.1', '3.0.1']
      - ['2.1.1', '2.1.1']

--- a/docs/index.md
+++ b/docs/index.md
@@ -36,8 +36,9 @@ To Run:
        * *'hg19-1.2.0'* = Human GRCh37 (hg19) release 84
        * *'mm10-3.0.0'* = Human GRCm38 (mm10) release 93
        * *'mm10-3.0.0'* = Human GRCm38 (mm10) release 84
-        * *'hg19_and_mm10-3.0.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 93
+        * *'GRCh38-and-mm10-3.1.0'* = Human GRCh38 + Mouse GRCm38 (mm10) release 93
-        * *'hg19_and_mm10-1.2.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84
+        * *'hg19_and_mm10-3.0.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm10) release 93
+        * *'hg19_and_mm10-1.2.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm10) release 84
        * *'ercc92-1.2.0'* = ERCC.92 Spike-In
  * **expect cells**
        * Expected number of recovered cells.

--- a/docs/references.md
+++ b/docs/references.md
@@ -4,7 +4,7 @@
  * Anaconda (Anaconda Software Distribution, [https://anaconda.com](https://anaconda.com))
 2. **cellranger**
-  * Cellranger mkfastq [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq)
+  * Cellranger count [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count)
 3. **MultiQc**:
  * Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:[10.1093/bioinformatics/btw354](https://dx.doi.org/10.1093/bioinformatics/btw354)

--- a/vizapp/functions.R
+++ b/vizapp/functions.R
+LoadData <- function(dim=c("pca","tsne","umap"),dir,samp){
+  exp <- readMM(paste0(dir,samp,"/outs/filtered_feature_bc_matrix/matrix.mtx.gz"))
+  features <- read.table(paste0(dir,samp,"/outs/filtered_feature_bc_matrix/features.tsv.gz"),quote="\t")
+  barcodes <- read.table(paste0(dir,samp,"/outs/filtered_feature_bc_matrix/barcodes.tsv.gz"),quote="\t")
+  exp.raw <- readMM(paste0(dir,samp,"/outs/raw_feature_bc_matrix/matrix.mtx.gz"))
+  features.raw <- read.table(paste0(dir,samp,"/outs/filtered_feature_bc_matrix/features.tsv.gz"),quote="\t")
+  barcodes.raw <- read.table(paste0(dir,samp,"/outs/raw_feature_bc_matrix/barcodes.tsv.gz"),quote="\t")
+  dr <- list()
+  for (i in dim){
+    if (i=="pca"){
+      dr[[i]] <- read.csv(paste0(dir,samp,"/outs/analysis/",i,"/10_components/projection.csv"))
+      dr[[i]] <- dr[[i]][,1:3]
+    } else {
+      dr[[i]] <- read.csv(paste0(dir,samp,"/outs/analysis/",i,"/2_components/projection.csv"))
+    }
+  }
+  rm(i)
+  cl <- c("graphclust",paste0("kmeans_",2:10,"_clusters"))
+  cluster <- list()
+  deg <- list()
+  for (i in cl){
+    cluster[[i]] <- read.csv(paste0(dir,samp,"/outs/analysis/clustering/",i,"/clusters.csv"))
+    deg[[i]] <- read.csv(paste0(dir,samp,"/outs/analysis/diffexp/",i,"/differential_expression.csv"))
+  }
+  rm(i)
+  qc <- read.csv(paste0(dir,samp,"/outs/metrics_summary.csv"))
+  qc <- data.frame(t(qc))
+  qc[,2] <- qc[,1]
+  qc[,1] <- rownames(qc)
+  qc <- qc[-1,]
+  colnames(qc) <- c("Metric","Value")
+  results <- list(
+    sample=samp,
+    exp=exp,
+    features=features,
+    barcodes=barcodes,
+    exp.raw=exp.raw,
+    features.raw=features.raw,
+    barcodes.raw=barcodes.raw,
+    dr=dr,
+    cluster=cluster,
+    deg=deg,
+    qc=qc
+  )
+  return(results)
+}
+Plot.cluster <- function(dr,cluster){
+  pl <-merge(dr,cluster,by="Barcode",all.x=TRUE)
+  axis.labs <- colnames(pl)[2:3]
+  colnames(pl)[2:3] <- c("dim1","dim2")
+  plot.out <- ggplot(pl,aes(x=dim1,y=dim2,col=factor(Cluster)))+geom_point()+scale_color_viridis(discrete=TRUE)+xlab(axis.labs[1])+ylab(axis.labs[2])+labs(col="Cluster")+theme_cowplot()
+  return(plot.out)
+}
+Plot.feature <- function(dr,ft){
+  dr$exp <- ft
+  axis.labs <- colnames(dr)[2:3]
+  colnames(dr)[2:3] <- c("dim1","dim2")
+  if (sum(dr$exp) != 0){
+    plot.out <- ggplot(dr,aes(x=dim1,y=dim2,col=exp))+geom_point()+scale_color_viridis(option="inferno")+xlab(axis.labs[1])+ylab(axis.labs[2])+labs(col="Expression")+theme_cowplot()
+  } else {
+    plot.out <- ggplot(dr,aes(x=dim1,y=dim2,col=exp))+geom_point()+scale_color_gradient(low="black",high="black")+xlab(axis.labs[1])+ylab(axis.labs[2])+labs(col="Expression")+theme_cowplot()
+  }
+  return(plot.out)
+}
+Plot.violinbox <- function(ft,cluster){
+  cluster$exp <- ft
+  cluster$Cluster <- factor(cluster$Cluster)
+  plot.out <- ggplot(cluster,aes(x=Cluster,y=exp,fill=Cluster))+geom_violin(scale="width",trim=TRUE)+geom_boxplot(width=0.25,fill="white",outlier.shape=NA)+scale_fill_viridis(discrete=TRUE)+ylab("Expression")+theme_cowplot()+theme(axis.text.x=element_text(angle=45))
+  return(plot.out)
+}
+Plot.cliffknee <- function(barcodes.raw,exp.raw,barcodes){
+  umi <- matrix(nrow=length(barcodes.raw[,1]),ncol=4)
+  umi[,1] <- t(colSums(exp.raw))
+  umi[,2] <- as.character(barcodes.raw[,1])
+  umi <- as.data.frame(umi)
+  umi[,1] <- as.numeric(levels(umi[,1]))[umi[,1]]
+  colnames(umi) <- c("nUMI","barcodes","rank","Cell")
+  umi <- umi[order(umi$nUMI,decreasing=TRUE),]
+  umi$rank <- 1:nrow(umi)
+  umi$Cell <- factor(as.character(umi$barcodes %in% barcodes[,1]))
+  umi$Cell <- factor(umi$Cell,levels(umi$Cell)[c(2,1)])
+  plot.out <- ggplot(umi,aes(x=rank,y=nUMI,col=Cell))+geom_point()+scale_color_manual(values=c("darkgreen","darkred"))+
+    scale_x_log10(breaks=trans_breaks("log10",function(x) 10^x),labels=trans_format("log10",math_format(10^.x)))+
+    scale_y_log10(breaks=trans_breaks("log10",function(x) 10^x),labels=trans_format("log10",math_format(10^.x)))+
+    annotation_logticks()+xlab("Barcode Rank")+ylab("nUMI")+theme_cowplot()
+  return(plot.out)
+}
--- a/vizapp/global.R
+++ b/vizapp/global.R
+library(shiny)
+library(shinythemes)
+library(Matrix)
+library(ggplot2)
+library(RColorBrewer)
+library(viridis)
+library(cowplot)
+library(scales)
+setwd("../")
+source("./vizapp/functions.R")
+#load data
+dir.shared <- "/work/BICF/s189701/cellranger_count/workflow/output/count310/"
+samples <- list.dirs(dir.shared,full.names=FALSE,recursive=FALSE)
+results <- LoadData(dim=c("umap","tsne","pca"),dir=dir.shared,samp=samples[1])
--- a/vizapp/server.R
+++ b/vizapp/server.R
-# This example implements a simple file browser for accessing results.
 library(shiny)
-library(shinyFiles)
+library(shinythemes)
+library(Matrix)
-# Results are available in the directory specified by the outputDir environment
+library(ggplot2)
-# variable, red by Sys.getenv
+library(RColorBrewer)
+library(viridis)
-rootdir <- Sys.getenv('outputDir')
+library(cowplot)
+library(scales)
-shinyServer(function(input, output, session) {
-    # The backend for a simple file chooser, restricted to the
-    # rootdir we obtained above.
-    # See https://github.com/thomasp85/shinyFiles
-    shinyFileChoose(input, 'files', roots=c('workflow'=rootdir), filetypes=c('', 'bed', 'xls','wig'), session=session)
+shinyServer(function(input,output,session){
+  #reactive inputs
+  values <- reactiveValues(
+    results=results,
+    dr.c="",cluster.c="",
+    dr.f="",feature.f="",
+    cluster.vb="",feature.vb="",
+    cluster.deg="",cluster.1.deg="",alpha.deg="",fc.deg="",direction.deg=""
+  )
+  values$results <- eventReactive(input$go.d,{
+    LoadData(dim=c("umap","tsne","pca"),dir=dir.shared,samp=input$sample)
+  })
+  output$loaded <- eventReactive(input$go.d,{
+    paste0("Sample ",values$results()$sample)
+  })
+  output$nav.analysis <- renderUI({
+    req(values$results()$sample)
+    tabsetPanel(type="tabs",
+      tabPanel("Cluster Plot",
+        sidebarPanel(
+          h3(textOutput("lab.sample.c")),
+          uiOutput("dr.c"),
+          uiOutput("cluster.c"),
+          actionButton("go.c","Submit")
+        ),
+        mainPanel(
+          h3(textOutput("lab.dr.c")),
+          h4(textOutput("lab.cluster.c")),
+          plotOutput("plot.cluster.c"),
+          tags$br(),
+          uiOutput("button.download.c")
+        )
+      ),
+      tabPanel("Feature Plot",
+        sidebarPanel(
+          h3(textOutput("lab.sample.f")),
+          uiOutput("dr.f"),
+          uiOutput("feature.f"),
+          actionButton("go.f","Submit")
+        ),
+        mainPanel(
+          h3(textOutput("lab.feature.f")),
+          h4(textOutput("lab.dr.f")),
+          plotOutput("plot.feature"),
+          tags$br(),
+          uiOutput("button.download.f")
+        )
+      ),
+      tabPanel("ViolinBox Plot",
+        sidebarPanel(
+          h3(textOutput("lab.sample.vb")),
+          uiOutput("cluster.vb"),
+          uiOutput("feature.vb"),
+          actionButton("go.vb","Submit"),
+          br(),
+          br(),
+          plotOutput("plot.cluster.vb")
+        ),
+        mainPanel(
+          h3(textOutput("lab.feature.vb")),
+          h4(textOutput("lab.cluster.vb")),
+          plotOutput("plot.violinbox"),
+          tags$br(),
+          uiOutput("button.download.vb"),
+          tags$br(),
+          tags$br(),
+          tableOutput("table.expression.vb")
+        )
+      ),
+      tabPanel("Differentially Expressed Features",
+        sidebarPanel(
+          h3(textOutput("lab.sample.deg")),
+          uiOutput("cluster.deg"),
+          uiOutput("cluster.1.deg"),
+          numericInput("alpha.deg","Maximum p-value",min=0,max =1,value=0.05,step=0.001),
+          numericInput("fc.deg","Minimum Fold Change",min=0,max =50,value=0,step=0.5),
+          radioButtons("direction.deg","Fold Change Direction",c("Positively Expressed"="up","Negatively Expressed"="down","Both"="both"),selected="up"),
+          actionButton("go.deg","Submit"),
+          br(),
+          br(),
+          plotOutput("plot.cluster.deg")
+        ),
+        mainPanel(
+          h3(textOutput("lab.cluster.1.deg")),
+          h4(textOutput("lab.cluster.deg")),
+          h5(textOutput("lab.alpha.deg")),
+          h5(textOutput("lab.fc.deg")),
+          uiOutput("download.deg.button"),
+          tags$br(),
+          tags$br(),
+          tableOutput("table.deg")
+        )
+      )
+    )
+  })
+  output$nav.qc <- renderUI({
+    req(values$results()$sample)
+    tabPanel("Output",
+      sidebarPanel(
+        h3(textOutput("lab.sample.qc")),
+        h4(textOutput("lab.cell.count")),
+        br(),
+        tableOutput("qc")
+      ),
+      mainPanel(
+        plotOutput("plot.cliffknee")
+      )
+    )
+  })
+  #sidebar input/outputs
+  output$lab.sample.c <- reactive({paste0("Sample ",values$results()$sample)})
+  output$dr.c <- renderUI({selectInput("dr.c","Dimentionality Reduction",names(values$results()$dr))})
+  output$cluster.c <- renderUI({selectInput("cluster.c","Clustering",names(values$results()$cluster))})
+  output$lab.sample.f <- reactive({paste0("Sample ",values$results()$sample)})
+  output$dr.f <- renderUI({selectInput("dr.f","Dimentionality Reduction",names(values$results()$dr))})
+  output$feature.f <- renderUI({textInput("feature.f","Feature",levels(values$results()$features[,2])[1])})
+  output$lab.sample.vb <- reactive({paste0("Sample ",values$results()$sample)})
+  output$cluster.vb <- renderUI({selectInput("cluster.vb","Clustering",names(values$results()$cluster))})
+  output$feature.vb <- renderUI({textInput("feature.vb","Feature",levels(values$results()$features[,2])[1])})
+  output$plot.cluster.vb <- renderPlot({
+    req(input$go.vb)
+    print(plot.cluster.vb())
+  })
+  output$lab.sample.deg <- reactive({paste0("Sample ",values$results()$sample)})
+  output$cluster.deg <- renderUI({selectInput("cluster.deg","Clustering",names(values$results()$cluster))})
+  output$cluster.1.deg <- renderUI({
+    clust <- levels(factor(values$results()$cluster[[req(input$cluster.deg)]]$Cluster))
+    selectInput("cluster.1.deg", "Specific Cluster",clust,clust[1])
+  })
+  observe({
+    if (!is.numeric(input$alpha.deg)) {
+      updateNumericInput(session,"alpha","Maximum p-value",min=0,max =1,value=0.05,step=0.001)
+    }
+  })
+  observe({
+    if (!is.numeric(input$fc.deg)) {
+      updateNumericInput(session,"fc","Minimum Fold Change",min=0,max =50,value=0,step=0.5)
+    }
+  })
+  output$lab.sample.qc <- reactive({paste0("Sample ",values$results()$sample)})
+  output$lab.cell.count <- renderText({paste0(nrow(values$results()$barcodes)," Cells Detected")})  
+  output$qc <- renderTable(values$results()$qc)
+  #main input/outputs
+  output$lab.dr.c <- eventReactive(input$go.c,{
+    req(input$go.c)
+    paste0(toupper(req(input$dr.c))," Reduction")
+  },ignoreNULL=FALSE)
+  output$lab.cluster.c <- eventReactive(input$go.c,{
+    req(input$go.c)
+    paste0(toupper(req(input$cluster.c))," Clustering")
+  },ignoreNULL=FALSE)
+  output$plot.cluster.c <- renderPlot({
+    req(input$go.c)
+    print(plot.cluster.c())
+  })
+  output$lab.feature.f <- eventReactive(input$go.f,{
+    req(input$go.f)
+    if(toupper(req(input$feature.f)) %in% as.character(values$results()$features[,2])){
+      toupper(req(input$feature.f))
+    } else {
+      paste0(req(input$feature.f)," NOT PRESENT")
+    }
+  },ignoreNULL=FALSE)
+  output$lab.dr.f <- eventReactive(input$go.f,{
+    req(input$go.f)
+    paste0(toupper(req(input$dr.f))," Reduction")
+  },ignoreNULL=FALSE)
+  output$plot.feature <- renderPlot({
+    req(input$go.f)
+    print(plot.feature())
+  })
+  output$lab.feature.vb <- eventReactive(input$go.vb,{
+    req(input$go.vb)
+    if(toupper(req(input$feature.vb)) %in% as.character(values$results()$features[,2])){
+      toupper(req(input$feature.vb))
+    } else {
+      paste0(req(input$feature.vb)," NOT PRESENT")
+    }
+  },ignoreNULL=FALSE)
+  output$lab.cluster.vb <- eventReactive(input$go.vb,{
+    req(input$go.vb)
+    paste0(toupper(req(input$cluster.vb))," Clustering")
+  },ignoreNULL=FALSE)
+  output$plot.violinbox <- renderPlot({
+    req(input$go.vb)
+    print(plot.violinbox())
+  })
+  output$table.expression.vb <- renderTable({
+    req(input$go.vb)
+    table.expression.vb()
+  })
+  output$lab.cluster.1.deg <- eventReactive(input$go.deg,{
+    req(input$go.deg)
+    paste0("Cluster ",req(input$cluster.1.deg)," DEGs")
+  },ignoreNULL=FALSE)
+  output$lab.cluster.deg <- eventReactive(input$go.deg,{
+    req(input$go.deg)
+    paste0(toupper(req(input$cluster.deg))," Clustering")
+  },ignoreNULL=FALSE)
+  output$lab.alpha.deg <- eventReactive(input$go.deg,{
+    req(input$go.deg)
+    paste0("Maximum p-value <- ",req(input$alpha.deg))
+  },ignoreNULL=FALSE)
+  output$lab.fc.deg <- eventReactive(input$go.deg,{
+    req(input$go.deg)
+    if (req(input$direction.deg) == "up"){
+      paste0("Minimum fold-change difference <- ",req(input$fc.deg)," above the other cells")
+    } else if (req(input$direction.deg) == "down") {
+      paste0("Minimum fold-change difference <- ",req(input$fc.deg)," below the other cells")
+    } else {
+      paste0("Minimum fold-change difference <- ",req(input$fc.deg)," above & below the other cells")
+    }
+  },ignoreNULL=FALSE)
+  output$table.deg <- renderTable({
+    req(input$go.deg)
+    table.deg()
+  })
+  output$plot.cluster.deg <- renderPlot({
+    req(input$go.deg)
+    print(plot.cluster.deg())
+  })
+  output$download.deg.button <- renderUI({
+    req(input$go.deg)
+    downloadButton("download.deg","Download Table")
+  })
+  output$plot.cliffknee <- renderPlot({print(Plot.cliffknee(barcodes.raw=values$results()$barcodes.raw,exp.raw=values$results()$exp.raw,barcodes=values$results()$barcodes))})
+  #reactive download buttons
+  output$button.download.c <- renderUI({
+    req(input$go.c)
+    downloadButton("download.c","Download Figure")
+  })
+  output$button.download.f <- renderUI({
+    req(input$go.f)
+    downloadButton("download.f","Download Figure")
+  })
+  output$button.download.vb <- renderUI({
+    req(input$go.vb)
+    downloadButton("download.vb","Download Figure")
+  })
+  output$button.download.deg <- renderUI({
+    req(input$go.deg)
+    downloadButton("download.deg","Download Table")
+  })
+  #save current parameters
+  values$dr.c <- eventReactive(input$go.c,{input$dr.c})
+  values$cluster.c <- eventReactive(input$go.c,{input$cluster.c})
+  values$dr.f <- eventReactive(input$go.f,{input$dr.f})
+  values$feature.f <- eventReactive(input$go.f,{toupper(input$feature.f)})
+  values$cluster.vb <- eventReactive(input$go.vb,{input$cluster.vb})
+  values$feature.vb <- eventReactive(input$go.vb,{toupper(input$feature.vb)})
+  values$cluster.deg <- eventReactive(input$go.deg,{input$cluster.deg})
+  values$cluster.1.deg <- eventReactive(input$go.deg,{input$cluster.1.deg})
+  values$alpha.deg <- eventReactive(input$go.deg,{input$alpha.deg})
+  values$fc.deg <- eventReactive(input$go.deg,{input$fc.deg})
+  values$direction.deg <- eventReactive(input$go.deg,{input$direction.deg})
+  #plot functions
+  plot.cluster.c <- eventReactive(input$go.c,{
+    Plot.cluster(
+    values$results()$dr[[req(input$dr.c)]],values$results()$cluster[[req(input$cluster.c)]])
+  },ignoreNULL=FALSE)
+  plot.feature <- eventReactive(input$go.f,{
+    if(toupper(req(input$feature.f)) %in% as.character(values$results()$features[,2])){
+      Plot.feature(values$results()$dr[[req(input$dr.f)]],values$results()$exp[as.numeric(rownames(values$results()$features[values$results()$features[,2]==toupper(req(input$feature.f)),])),])
+    } else {
+      plot.new()
+    }
+  },ignoreNULL=FALSE)
+  plot.violinbox <- eventReactive(input$go.vb,{
+    if(toupper(req(input$feature.vb)) %in% as.character(values$results()$features[,2])){
+      Plot.violinbox(values$results()$exp[as.numeric(rownames(values$results()$features[values$results()$features[,2]==toupper(req(input$feature.vb)),])),],values$results()$cluster[[req(input$cluster.vb)]])
+    } else {
+      plot.new()
+    }
+  },ignoreNULL=FALSE)
+  plot.cluster.vb <- eventReactive(input$go.vb,{
+    Plot.cluster(
+      values$results()$dr[["umap"]],values$results()$cluster[[req(input$cluster.vb)]])
+  },ignoreNULL=FALSE)
+  plot.cluster.deg <- eventReactive(input$go.deg,{
+    req(input$cluster.1.deg)
+    Plot.cluster(
+      values$results()$dr[["umap"]],values$results()$cluster[[input$cluster.deg]])
+  },ignoreNULL=FALSE)
+  #table functions
+  table.expression.vb <- eventReactive(input$go.vb,{
+    if(toupper(req(input$feature.vb)) %in% as.character(values$results()$features[,2])){
+      tab <- values$results()$deg[[req(input$cluster.vb)]][values$results()$deg[[req(input$cluster.vb)]][,2]==toupper(req(input$feature.vb)),c(2,grep("Mean.Counts",names(values$results()$deg[[req(input$cluster.vb)]])))]
+      colnames(tab) <- c("Feature",gsub(".Mean.Counts","",names(tab[,-1])))
+      tab <- data.frame(t(tab))
+      tab[,2] <- tab[,1]
+      tab[,1] <- rownames(tab)
+      tab <- tab[-1,]
+      colnames(tab) <- c("Cluster",paste0("Ave ",req(input$feature.vb)," Expression"))
+      tab
+    } else {
+      ""
+    }
+  },ignoreNULL=FALSE)
+  table.deg <- eventReactive(input$go.deg,{
+    tab <- values$results()$deg[[input$cluster.deg]]
+    tab <- tab[tab[paste0("Cluster.",req(input$cluster.1.deg),".Adjusted.p.value")]<=input$alpha.deg,]
+    if (input$fc.deg == 0){
+      fc <- 0
+    } else {
+      fc <- log2(input$fc.deg)
+    }
+    if (input$direction.deg=="up"){
+      tab <- tab[tab[paste0("Cluster.",req(input$cluster.1.deg),".Log2.fold.change")]>=fc,]
+    } else if (input$direction.deg=="down"){
+      tab <- tab[tab[paste0("Cluster.",req(input$cluster.1.deg),".Log2.fold.change")]<=-fc,]
+    } else {
+      tab <- tab[tab[paste0("Cluster.",req(input$cluster.1.deg),".Log2.fold.change")]>=fc | tab[paste0("Cluster.",req(input$cluster.1.deg),".Log2.fold.change")]<=-fc,]
+    }
+    tab <- tab[,c(colnames(values$results()$deg[[input$cluster.deg]])[2],paste0("Cluster.",req(input$cluster.1.deg),".Mean.Counts"),paste0("Cluster.",req(input$cluster.1.deg),".Log2.fold.change"),paste0("Cluster.",req(input$cluster.1.deg),".Adjusted.p.value"))]
+    tab <- tab[order(abs(tab[paste0("Cluster.",req(input$cluster.1.deg),".Log2.fold.change")]),decreasing=TRUE),]
+    tab
+  },ignoreNULL=FALSE)
+  #download
+  output$download.c <- downloadHandler(
+    filename <- function(){paste0("clusters_",values$dr.c(),"_",values$cluster.c(),".pdf")},
+    content <- function(file){
+      pdf(file,onefile=FALSE)
+      print(plot.cluster.c())
+      dev.off()
+    }
+  )
+  output$download.f <- downloadHandler(
+    filename <- function(){paste0("feature_",values$dr.f(),"_",toupper(values$feature.f()),".pdf")},
+    content <- function(file){
+      pdf(file,onefile=FALSE)
+      print(plot.feature())
+      dev.off()
+    }
+  )
+  output$download.vb <- downloadHandler(
+    filename <- function(){paste0("violinbox_",values$cluster.vb(),"_",toupper(values$feature.vb()),".pdf")},
+    content <- function(file){
+      pdf(file,onefile=FALSE)
+      print(plot.violinbox())
+      dev.off()
+    }
+  )
+  output$download.deg <- downloadHandler(
+    filename <- function(){paste0("deg_",values$cluster.deg(),"_cluster.",values$cluster.1.deg(),"_p",values$alpha.deg(),"_fc",values$fc.deg(),values$direction.deg(),".csv")},
+    content <- function(file){
+      write.csv(table.deg(),file,row.names=FALSE,quote=FALSE)
+    }
+  )
 })
--- a/vizapp/ui.R
+++ b/vizapp/ui.R
-library(shiny)
+navbarPage(theme=shinytheme("slate"),"BICF Cellranger Count Analysis (cellranger 3.1.0 version)",
-library(shinyFiles)
+  tabPanel("Select Data",
+    mainPanel(
+      selectInput("sample","Available Samples",samples),
-shinyUI(fluidPage(
+      actionButton("go.d","Load"),
+      br(),
-  verticalLayout(
+      br(),
+      h4("Please whait until the sample has been loaded and a message below displays this, it may take a few minutes"),
-    # Application title
+      h3(textOutput("loaded"))
-    titlePanel("Astrocyte Example"),
-    wellPanel(
-        helpText("This is a minimal example, demonstrating how
-        a Shiny visualization application can access the output of a workflow.
-        Here we provide a file browser using the shinyFiles package. Real
-        Astrocyte vizapps would provide custom methods to access and visualize
-        output."),
-        helpText("The workflow output is in the directory set in the
-        outputDir environment variable. this can be retrieved in R with the
-        command Sys.getenv('outputDir')"),
-        # A simple file browser within the workflow output directory
-        # See https://github.com/thomasp85/shinyFiles
-        shinyFilesButton('files', label='Browse workflow output', title='Please select a file', multiple=FALSE)
    )
+  ),
+  tabPanel("Analysis",
+    uiOutput("nav.analysis")
+  ),
+  tabPanel("QC",
+    uiOutput("nav.qc")
  )
-))
+)
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -18,6 +18,10 @@ process {
    module = ['cellranger/3.0.2']
    queue = '128GB,256GB,256GBv1,384GB'
  }
+  withLabel: count310 {
+    module = ['cellranger/3.1.0']
+    queue = '128GB,256GB,256GBv1,384GB'
+  }
  withLabel: versions {
    module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
    executor = 'local'
@@ -49,6 +53,9 @@ params {
    'mm10-1.2.0' {
      loc = '/project/apps_database/cellranger/refdata-cellranger-'
    }
+    'GRCh38_and_mm10-3.1.0' {
+      loc = '/project/apps_database/cellranger/refdata-cellranger-'
+    }
    'hg19_and_mm10-3.0.0' {
      loc = '/project/apps_database/cellranger/refdata-cellranger-'
    }

--- a/workflow/main.nf
+++ b/workflow/main.nf
 #!/usr/bin/env nextflow
+/*
-// Path to an input file, or a pattern for multiple inputs
+main.nf
-// Note - $baseDir is the location of this workflow file main.nf
+*
+* --------------------------------------------------------------------------
+* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+* --------------------------------------------------------------------------
+*
+*/
 // Define Input variables
 params.name = "run"
@@ -11,7 +16,7 @@ params.genome = 'GRCh38-3.0.0'
 params.expectCells = 10000
 params.forceCells = 0
 params.kitVersion = 'three'
-params.version = '3.0.2'
+params.version = '3.1.0'
 params.astrocyte = false
 params.outDir = "${baseDir}/output"
 params.multiqcConf = "${baseDir}/conf/multiqc_config.yaml"
@@ -64,6 +69,7 @@ outDir = params.outDir
 multiqcConf = params.multiqcConf
 references = params.references
 process checkDesignFile {
  tag "${name}"
@@ -100,20 +106,25 @@ samples.into {
  samples211
  samples301
  samples302
+  samples310
 }
 refLocation.into {
  refLocation211
  refLocation301
  refLocation302
+  refLocation310
 }
 expectCells211 = expectCells
 expectCells301 = expectCells
 expectCells302 = expectCells
+expectCells310 = expectCells
 forceCells211 = forceCells
 forceCells301 = forceCells
 forceCells302 = forceCells
+forceCells310 = forceCells
 chemistryParam301 = chemistryParam
 chemistryParam302 = chemistryParam
+chemistryParam310 = chemistryParam
 process count211 {
@@ -143,7 +154,7 @@ process count211 {
      ulimit -a
      bash ${baseDir}/scripts/filename_check.sh -r ${ref}
      cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells211}
-      sed -E 's/("([^"]*)")?,/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
+      sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
      """
    } 
    else {
@@ -152,7 +163,7 @@ process count211 {
      ulimit -a
      bash ${baseDir}/scripts/filename_check.sh -r ${ref}
      cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --force-cells=${forceCells211}
-      sed -E 's/("([^"]*)")?,/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
+      sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
      """
    }
@@ -187,7 +198,7 @@ process count301 {
      ulimit -a
      bash ${baseDir}/scripts/filename_check.sh -r ${ref}
      cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells301} --chemistry=${chemistryParam301}
-      sed -E 's/("([^"]*)")?,/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
+      sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
      """
    } 
    else {
@@ -196,7 +207,7 @@ process count301 {
      ulimit -a
      bash ${baseDir}/scripts/filename_check.sh -r ${ref}
      cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --force-cells=${forceCells301} --chemistry=${chemistryParam301}
-      sed -E 's/("([^"]*)")?,/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
+      sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
      """
    }
@@ -231,7 +242,7 @@ process count302 {
      ulimit -a
      bash ${baseDir}/scripts/filename_check.sh -r ${ref}
      cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells302} --chemistry=${chemistryParam302}
-      sed -E 's/("([^"]*)")?,/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
+      sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
      """
    } 
    else {
@@ -240,7 +251,51 @@ process count302 {
      ulimit -a
      bash ${baseDir}/scripts/filename_check.sh -r ${ref}
      cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --force-cells=${forceCells302} --chemistry=${chemistryParam302}
-      sed -E 's/("([^"]*)")?,/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
+      sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
+      """
+    }
+}
+process count310 {
+  queue '128GB,256GB,256GBv1,384GB'
+  tag "${sample}"
+  publishDir "${outDir}/${task.process}", mode: 'copy'
+  module 'cellranger/3.1.0'
+  input:
+    set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz") from samples310
+    file ref from refLocation310.first()
+    expectCells310
+    forceCells310
+    chemistryParam310
+  output:
+    file("**/outs/**") into outPaths310
+    file("*_metrics_summary.tsv") into metricsSummary310
+  when:
+    version == '3.1.0'
+  script:
+    if (forceCells310 == 0) {
+      """
+      hostname
+      ulimit -a
+      bash ${baseDir}/scripts/filename_check.sh -r ${ref}
+      cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells310} --chemistry=${chemistryParam310}
+      sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
+      """
+    }
+    else {
+      """
+      hostname
+      ulimit -a
+      bash ${baseDir}/scripts/filename_check.sh -r ${ref}
+      cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --force-cells=${forceCells310} --chemistry=${chemistryParam310}
+      sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
      """
    }
@@ -272,10 +327,9 @@ process versions {
 }
-metricsSummary = metricsSummary211.mix(metricsSummary301, metricsSummary302)
+metricsSummary = metricsSummary211.mix(metricsSummary301, metricsSummary302, metricsSummary310)
-// Generate MultiQC Report
 process multiqc {
  tag "${name}"
@@ -299,4 +353,4 @@ process multiqc {
    multiqc -c ${multiqcConf} .
    """
 }
\ No newline at end of file
--- a/workflow/scripts/check_design.py
+++ b/workflow/scripts/check_design.py
 #!/usr/bin/env python3
+#check_design.py
-'''Check if design file is correctly formatted and matches files list.'''
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 import argparse
 import logging
@@ -11,8 +15,6 @@ For more details:
        %(prog)s --help
 '''
-# SETTINGS
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())
 logger.propagate = False
@@ -61,6 +63,7 @@ def check_design_headers(design):
    return design
 def check_files(design, fastq):
    '''Check if design file has the files found.'''
@@ -104,4 +107,4 @@ def main():
    new_design_df.to_csv('design.checked.csv', header=True, sep=',', index=False)
 if __name__ == '__main__':
    main()
\ No newline at end of file
--- a/workflow/scripts/filename_check.sh
+++ b/workflow/scripts/filename_check.sh
 #!/bin/bash
 #filename_check.sh
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 usage() {
  echo "-r  --ref file"
@@ -28,4 +33,4 @@ if [ $(echo "${ref}" | tr -d ' ') != "${ref}" ]; then
  echo "Error: Spaces found in Reference Files"
  echo ${ref}
  exit 21
 fi
\ No newline at end of file
--- a/workflow/scripts/generate_references.py
+++ b/workflow/scripts/generate_references.py
 #!/usr/bin/env python3
+#generate_references.py
-'''Make header for HTML of references.'''
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 import argparse
 import subprocess
@@ -12,8 +16,6 @@ For more details:
        %(prog)s --help
 '''
-# SETTINGS
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())
 logger.propagate = False
@@ -65,4 +67,4 @@ def main():
 if __name__ == '__main__':
    main()
\ No newline at end of file
--- a/workflow/scripts/generate_versions.py
+++ b/workflow/scripts/generate_versions.py
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
+#generate_versions.py
+#*
-'''Make YAML of software versions.'''
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 from __future__ import print_function
 from collections import OrderedDict
@@ -15,7 +18,6 @@ For more details:
        %(prog)s --help
 '''
-# SETTINGS
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())
 logger.propagate = False
@@ -104,4 +106,4 @@ def main():
 if __name__ == '__main__':
    main()
\ No newline at end of file
--- a/workflow/tests/test_check_design.py
+++ b/workflow/tests/test_check_design.py
 #!/usr/bin/env python3
+#test_check_design.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 import pytest
 import pandas as pd
@@ -19,3 +25,7 @@ def test_count301_design():
 @pytest.mark.count302
 def test_count302_design():
    assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))
+@pytest.mark.count310
+def test_count310_design():
+    assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))
\ No newline at end of file
--- a/workflow/tests/test_count.py
+++ b/workflow/tests/test_count.py
 #!/usr/bin/env python3
+#test_count.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 import pytest
 import pandas as pd
@@ -23,3 +29,8 @@ def test_count301_count():
 def test_count302_count():
    assert os.path.exists(os.path.join(test_output_path, 'count302', 'sample1_metrics_summary.tsv'))
    assert os.path.exists(os.path.join(test_output_path, 'count302', 'sample1', 'outs'))
+@pytest.mark.count310
+def test_count310_count():
+    assert os.path.exists(os.path.join(test_output_path, 'count310', 'sample1_metrics_summary.tsv'))
+    assert os.path.exists(os.path.join(test_output_path, 'count310', 'sample1', 'outs'))
\ No newline at end of file
--- a/workflow/tests/test_multiqc.py
+++ b/workflow/tests/test_multiqc.py
 #!/usr/bin/env python3
+#test_multiqc.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 import pytest
 import pandas as pd
@@ -19,3 +25,7 @@ def test_count301_multiqc():
 @pytest.mark.count302
 def test_count302_multiqc():
    assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html'))
+@pytest.mark.count310
+def test_count310_multiqc():
+    assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html'))
\ No newline at end of file