Fix output for plotViolinBox

workflow/nextflow.config

 profiles {
   standard {
-    includeConfig 'conf/biohpc_local.config'
+    includeConfig 'conf/biohpc.config'
   }
 }

workflow/scripts/plotViolinBox.R

@@ -32,15 +32,21 @@ chunk <- read.csv(opt$c,header=FALSE)
 exp <- exp[exp$genes %in% chunk$V1,]
 
 #Create output folders
-if (!dir.exists(paste0("./",opt$g))){
-  dir.create(paste0("./",opt$g))
+if (!dir.exists("./ViolinBox")){
+  dir.create("./ViolinBox",opt$g)
+}
+if (!dir.exists(paste0("./ViolinBox/",opt$g))){
+  dir.create(paste0("./ViolinBox/",opt$g))
+}
+if (!dir.exists(paste0("./ViolinBox/",opt$g,"/genes"))){
+  dir.create(paste0("./ViolinBox/",opt$g,"/genes"))
 }
 
 #Plot
 for (i in chunk$V1){
   id.exp <- id
   id.exp$Expression <- as.numeric(exp[which(exp$genes==i),])[-ncol(exp)]
-  png(paste0("./",opt$g,"/",i,".png"),width=1000,height=500,bg="white")
+  png(paste0("./ViolinBox/",opt$g,"/genes/",i,"_1.png"),width=1000,height=500,bg="white")
   plot(ggplot(id.exp,aes_string(x=opt$g,y="Expression",fill=opt$g))+geom_violin(scale="width",trim=TRUE)+labs(y="Expression")+geom_boxplot(width=0.25,fill="white",outlier.shape=NA)+theme_cowplot())
   dev.off()
   rm(id.exp)

workflow/scrna-seq_imgen.nf

@@ -203,7 +203,7 @@ process plotFeature {
 * plotViolinBox: plot violin/box plots in gene chunks
 */
 process plotViolinBox {
-    publishDir "${outDir}/png/ViolinBox", mode: 'move', overwrite: true
+    publishDir "${outDir}", mode: 'move', overwrite: true
 
     input:
     file matrix_plotViolinBox

workflow/scrna-seq_imgen_test.nf

-#!/usr/bin/env nextflow
-
-// Define input variables
-params.rda = "${baseDir}/../test_data/sc10x.rda"
-params.seurat = "sc10x"
-params.tsne = true
-params.umap = true
-params.assay = "RNA"
-params.slot = "scale.data"
-params.scale = true
-params.sample = 100
-params.groups = "${baseDir}/../test_data/groups.txt"
-params.convert = "GRCh38p5"
-
-params.studyIID = "studyIID"
-params.applicationName = "applicationName"
-
-params.outDir = "${baseDir}/../output"
-
-// Parse input variables
-rda = Channel.fromPath(params.rda)
-rda.into {
-    rda_createMatrix
-    rda_createGroup
-}
-seurat_createMatrix = params.seurat
-seurat_createGroup = params.seurat
-tsne_createMatrix = params.tsne
-tsne_plotIdentGroup = params.tsne
-tsne_plotFeature = params.tsne
-umap_createMatrix = params.umap
-umap_plotIdentGroup = params.umap
-umap_plotFeature = params.umap
-assay = params.assay
-slot = params.slot
-scale = params.scale
-sample = params.sample
-groups_createGroup = file(params.groups).readLines()
-groups_plotIdentGroup = file(params.groups).readLines()
-groups_plotViolinPlot = file(params.groups)
-convert = params.convert
-
-outDir = "${params.outDir}/deriva/Seq/${params.studyIID}/application_files/${params.applicationName}"
-logsDir = "${params.outDir}/Logs"
-
-/*
-* createMatrix: extract cell/gene matrix from Seurat object
-*/
-process createMatrix {
-    tag "${seurat_createMatrix}"
-
-    input:
-    file rda_createMatrix
-    val seurat_createMatrix
-    val tsne_createMatrix
-    val umap_createMatrix
-    val assay
-    val slot
-    val scale
-    val sample
-
-    output:
-    file("matrix/*") into matrixRaw
-    file("cells.csv") into cells
-
-    script:
-    """
-    hostname
-    ulimit -a
-    module load seurat/3.0.0
-    seurat-Rscript ${baseDir}/scripts/createMatrix.R --r ${rda_createMatrix} --o ${seurat_createMatrix} --t ${tsne_createMatrix} --u ${umap_createMatrix} --a ${assay} --s ${slot} --l ${scale} --p ${sample}
-    """
-}
-
-/*
-* createGroup: extract ident groups from Seurat object
-*/
-process createGroup {
-    tag "${group_createGroup}"
-
-    input:
-    file rda_createGroup
-    val seurat_createGroup
-    each group_createGroup from groups_createGroup
-    file cells
-    
-    output:
-    file("*") into id
-
-    script:
-    """
-    hostname
-    ulimit -a
-    module load seurat/3.0.0
-    seurat-Rscript ${baseDir}/scripts/createGroup.R --r ${rda_createGroup} --o ${seurat_createGroup} --g ${group_createGroup}
-    """
-}
-
-//Duplicate group IDs
-id.into {
-    id_plotIdentGroup
-    id_plotViolinBox
-}
-
-/*
-* renameGenes: convert gene symbols to NCBI ID's for GUDMAP/RBK
-*/
-process renameGenes {
-    tag "NCBI"
-
-    input:
-    file matrixRaw
-    val convert
-
-    output:
-    file("*") into matrixFinal 
-    file("genes.csv") into genes
-
-
-    script:
-    if (convert == "NO"){
-        """
-        hostname
-        ulimit -a
-        cp -R ./raw/*.mtx .
-        cp -R ./raw/*.csv .
-        """
-    } else {
-        """
-        hostname
-        ulimit -a
-        cp -R ./raw/*.csv .
-        module load seurat/3.0.0
-        seurat-Rscript ${baseDir}/scripts/renameGenes.R --g ${convert}
-        """
-    }
-}
-
-// Duplicate matrix files
-matrixFinal.into {
-    matrix_plotIdentGroup
-    matrix_plotFeature
-    matrix_plotViolinBox
-}
-
-/*
-* plotIdentGroup: plot identity groups in reduced dimensions
-*/
-process plotIdentGroup {
-    tag "${group_plotIdentGroup}"
-    publishDir "${outDir}", mode: 'move', overwrite: true
-
-    input:
-    file matrix_plotIdentGroup
-    file("*") from id_plotIdentGroup.collect()
-    each group_plotIdentGroup from groups_plotIdentGroup
-    val tsne_plotIdentGroup
-    val umap_plotIdentGroup
-
-    output:
-    file("**/*.png") into plotsIdentGroup
-
-    script:
-    """
-    hostname
-    ulimit -a
-    module load seurat/3.0.0
-    seurat-Rscript ${baseDir}/scripts/plotIdentGroup.R --g ${group_plotIdentGroup} --t ${tsne_plotIdentGroup} --u ${umap_plotIdentGroup}
-    """
-}
-
-// Split genes into chunks
-genes.splitText(by: 1000).into {
-    genesChunks_plotFeature
-    genesChunks_plotViolinBox
-}
-
-/*
-* plotFeature: plot feature plots in gene chunks
-*/
-process plotFeature {
-    publishDir "${outDir}", mode: 'move', overwrite: true
-
-    input:
-    file matrix_plotFeature
-    each file(chunk) from genesChunks_plotFeature
-    val tsne_plotFeature
-    val umap_plotFeature
-
-    output:
-    file("**/*.png") into plotsFeature
-
-    script:
-    """
-    hostname
-    ulimit -a
-    module load seurat/3.0.0
-    seurat-Rscript ${baseDir}/scripts/plotFeature.R --t ${tsne_plotFeature} --u ${umap_plotFeature} --c ${chunk}
-    """
-}
\ No newline at end of file