diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 791ef96be43a9ba90e9ef57e51a8e89a7f17091a..03a422fc78ecb76ac0bae7962cda596acec7e15b 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -36,16 +36,19 @@ simple_1:
- branches
- tags
except:
- - develop
- - master
+ refs:
+ - 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'
- - pytest -m count302
+ - 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 count310
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- .nextflow.log
+ - workflow/output/count310/sample1/outs/web_summary.html
+ - workflow/output/multiqc/run/multiqc_report.html
expire_in: 2 days
retry:
max: 1
@@ -57,17 +60,20 @@ simple_2:
only:
- branches
except:
- - develop
- - master
- - tags
+ refs:
+ - develop
+ - master
+ - tags
script:
- - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v3s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.1'
- - pytest -m count301
+ - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v3s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.1.0'
+ - pytest -m count310
artifacts:
name: "$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'
- - pytest -m count302
+ - 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 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
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3e2d478d74f3bd8cfaae2ea4be9eba073a8dfcef..df4bdebb1180a5eb2ed19928d12262bf84bd551e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,18 @@
-# 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
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000000000000000000000000000000000000..ce31415967a482f717d2e7eaea440fd34d4e9ba6
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,25 @@
+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.
diff --git a/README.md b/README.md
index 6892ea715becad0d2669be7313747d5679e6c85f..6323ec5b79b16f933558813f4c745cba11be01ef 100755
--- 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
- * *'hg19_and_mm10-1.2.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84
+ * *'GRCh38_and_mm10-3.1.0'* = Human GRCh38 + Mouse GRCm38 (mm10) release 93
+ * *'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:
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 0c7a0a05e2792dc8ead17dd738c0135d19ec911a..1a7cb7a0cf81e44d4f67198cc57b5ad91fdd3820 100755
--- 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']
- - ['hg19_and_mm10-1.2.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84']
+ - ['GRCh38_and_mm10-3.1.0', 'Human GRCh38 + Mouse GRCm38 (mm10) release 93']
+ - ['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']
diff --git a/docs/index.md b/docs/index.md
index b2c1ad6c49707a7c493a047c659b3c1cf42acd7f..29cf0d399120909478055abf5538241312f28a40 100644
--- 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
- * *'hg19_and_mm10-1.2.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84
+ * *'GRCh38-and-mm10-3.1.0'* = Human GRCh38 + Mouse GRCm38 (mm10) release 93
+ * *'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.
diff --git a/docs/references.md b/docs/references.md
index d2034fbff9592f59bbf2c281c79d3da075cda008..ea483c496889564a214e995e17e2b56e4991a557 100644
--- 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)
diff --git a/vizapp/functions.R b/vizapp/functions.R
new file mode 100644
index 0000000000000000000000000000000000000000..8e30560bfb52c279fa4dc4158880f96ae7e40567
--- /dev/null
+++ b/vizapp/functions.R
@@ -0,0 +1,98 @@
+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)
+}
diff --git a/vizapp/global.R b/vizapp/global.R
new file mode 100644
index 0000000000000000000000000000000000000000..988fc942d71c2db605dec0e86e2d8504ae2b06f7
--- /dev/null
+++ b/vizapp/global.R
@@ -0,0 +1,16 @@
+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])
diff --git a/vizapp/server.R b/vizapp/server.R
index 81017c8445db8d640af1798cc8160bdffe2ec789..595710378f2ad30ed97394052d217f11e424f2e9 100644
--- a/vizapp/server.R
+++ b/vizapp/server.R
@@ -1,20 +1,365 @@
-# This example implements a simple file browser for accessing results.
-
library(shiny)
-library(shinyFiles)
-
-# Results are available in the directory specified by the outputDir environment
-# variable, red by Sys.getenv
-
-rootdir <- Sys.getenv('outputDir')
-
-
-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)
+library(shinythemes)
+library(Matrix)
+library(ggplot2)
+library(RColorBrewer)
+library(viridis)
+library(cowplot)
+library(scales)
+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)
+ }
+ )
})
diff --git a/vizapp/ui.R b/vizapp/ui.R
index 79f4cc99131a5d5dcb3d0e4694650db178ed8c5c..e1a6a90180d0d05ba63922ff567ba566efe53b8e 100644
--- a/vizapp/ui.R
+++ b/vizapp/ui.R
@@ -1,30 +1,18 @@
-library(shiny)
-library(shinyFiles)
-
-
-shinyUI(fluidPage(
-
- verticalLayout(
-
- # Application title
- 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)
-
+navbarPage(theme=shinytheme("slate"),"BICF Cellranger Count Analysis (cellranger 3.1.0 version)",
+ tabPanel("Select Data",
+ mainPanel(
+ selectInput("sample","Available Samples",samples),
+ actionButton("go.d","Load"),
+ br(),
+ br(),
+ h4("Please whait until the sample has been loaded and a message below displays this, it may take a few minutes"),
+ h3(textOutput("loaded"))
)
+ ),
+ tabPanel("Analysis",
+ uiOutput("nav.analysis")
+ ),
+ tabPanel("QC",
+ uiOutput("nav.qc")
)
-))
+)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 6e356466fb53801aa9c00876f55bfc6903798c50..a5ea037bbdc5558ff20dec18c238ffa4e3f4ed44 100755
--- 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-'
}
diff --git a/workflow/main.nf b/workflow/main.nf
index e0e2f551111de61d27d892fa8ab0883c84ec4b4b..8862991d57eec85dae8d55ecc7ac7001a187e671 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -1,7 +1,12 @@
#!/usr/bin/env nextflow
-
-// Path to an input file, or a pattern for multiple inputs
-// Note - $baseDir is the location of this workflow file main.nf
+/*
+main.nf
+*
+* --------------------------------------------------------------------------
+* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+* --------------------------------------------------------------------------
+*
+*/
// Define Input variables
params.name = "run"
@@ -11,7 +16,7 @@ params.genome = 'GRCh38-3.0.0'
params.expectCells = 10000
params.forceCells = 0
params.kitVersion = 'three'
-params.version = '3.0.2'
+params.version = '3.1.0'
params.astrocyte = false
params.outDir = "${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
diff --git a/workflow/scripts/check_design.py b/workflow/scripts/check_design.py
index a648a4e20d4a79b52cad60d6415bed14cf39fda9..c5c679e58b2819e6fafb4f34e6181cdd62f8cdbd 100755
--- a/workflow/scripts/check_design.py
+++ b/workflow/scripts/check_design.py
@@ -1,6 +1,10 @@
#!/usr/bin/env python3
-
-'''Check if design file is correctly formatted and matches files list.'''
+#check_design.py
+#*
+#* --------------------------------------------------------------------------
+#* 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()
+ main()
\ No newline at end of file
diff --git a/workflow/scripts/filename_check.sh b/workflow/scripts/filename_check.sh
index 78fa08ed25b54c1e3f921819a1b485525c772abf..333bb7ad2b0a3dce27675d3ea09e9c585aa42eff 100644
--- a/workflow/scripts/filename_check.sh
+++ b/workflow/scripts/filename_check.sh
@@ -1,5 +1,10 @@
#!/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
+fi
\ No newline at end of file
diff --git a/workflow/scripts/generate_references.py b/workflow/scripts/generate_references.py
index c40cc7efa689e8b4d8fcd52908ffe7a8112d3e8c..e614db7b3c22c1ea139f2cfac1f25d4780041df6 100755
--- a/workflow/scripts/generate_references.py
+++ b/workflow/scripts/generate_references.py
@@ -1,6 +1,10 @@
#!/usr/bin/env python3
-
-'''Make header for HTML of references.'''
+#generate_references.py
+#*
+#* --------------------------------------------------------------------------
+#* 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()
+ main()
\ No newline at end of file
diff --git a/workflow/scripts/generate_versions.py b/workflow/scripts/generate_versions.py
index 242c971b4ca8769e13c9dfb16d4be092bc8ea86b..ddcda535f6bf1f8350f5aa148af517f2c421c272 100755
--- a/workflow/scripts/generate_versions.py
+++ b/workflow/scripts/generate_versions.py
@@ -1,7 +1,10 @@
#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-'''Make YAML of software versions.'''
+#generate_versions.py
+#*
+#* --------------------------------------------------------------------------
+#* 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()
+ main()
\ No newline at end of file
diff --git a/workflow/tests/test_check_design.py b/workflow/tests/test_check_design.py
index 28968b0dbf1ab4bca46df91ec1d7e23812b47e9d..f425d09ab3a19ba1e610f451435a657f55d954ae 100644
--- a/workflow/tests/test_check_design.py
+++ b/workflow/tests/test_check_design.py
@@ -1,4 +1,10 @@
#!/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
diff --git a/workflow/tests/test_count.py b/workflow/tests/test_count.py
index b1bafe439b74fbe84e88f891e28e7880d653b1c3..86623ca6057dd298ae0294caa1b6ce91d32296ad 100644
--- a/workflow/tests/test_count.py
+++ b/workflow/tests/test_count.py
@@ -1,4 +1,10 @@
#!/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
diff --git a/workflow/tests/test_multiqc.py b/workflow/tests/test_multiqc.py
index d625e4088219cc3f875d1e55e7d17d3153e017e7..7ca8d237484434e83052e1b38b7b232cb59b2740 100644
--- a/workflow/tests/test_multiqc.py
+++ b/workflow/tests/test_multiqc.py
@@ -1,4 +1,10 @@
#!/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
diff --git a/workflow/tests/test_versions.py b/workflow/tests/test_versions.py
index 07a233c459c087051441780f1d0a42d00f6c6d65..535e029ffc5f9a1d0eadc63b286397c81a2427c0 100644
--- a/workflow/tests/test_versions.py
+++ b/workflow/tests/test_versions.py
@@ -1,4 +1,10 @@
#!/usr/bin/env python3
+#test_versions.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* --------------------------------------------------------------------------
+#*
import pytest
import pandas as pd
@@ -22,3 +28,8 @@ def test_count301_versions():
def test_count302_versions():
assert os.path.exists(os.path.join(test_output_path, 'versions_mqc.yaml'))
assert os.path.exists(os.path.join(test_output_path, 'references_mqc.yaml'))
+
+@pytest.mark.count310
+def test_count310_versions():
+ assert os.path.exists(os.path.join(test_output_path, 'versions_mqc.yaml'))
+ assert os.path.exists(os.path.join(test_output_path, 'references_mqc.yaml'))
\ No newline at end of file