Fix output for plotIdentGroup

workflow/conf/biohpc_local.config

+process {
+  executor = 'local'
+
+  // Process specific configuration
+
+}
+
+
+trace {
+  enabled = true
+  file = 'pipeline_trace.txt'
+  fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
+}
+
+timeline {
+  enabled = true
+  file = 'timeline.html'
+}
+
+report {
+  enabled = true
+  file = 'report.html'
+}
+
+tower {
+  accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
+  enabled = true
+}
+
+singularity {
+  enabled = true
+  cacheDir = '/project/shared/bicf_workflow_ref/singularity_images/'
+}
+
+env {
+  http_proxy = 'http://proxy.swmed.edu:3128'
+  https_proxy = 'http://proxy.swmed.edu:3128'
+  all_proxy = 'http://proxy.swmed.edu:3128'
+}

workflow/nextflow.config

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

workflow/scripts/plotIdentGroup.R

@@ -19,15 +19,17 @@ rm(option_list)
 id <- read.csv(paste0("./group_",opt$g,".csv"),header=FALSE)
 names(id)[2] <- opt$g
 
+#Create output folders
+if (!dir.exists(paste0("./",opt$g))){
+  dir.create(paste0("./",opt$g))
+}
+
 #Load dr and plot
 if (opt$t == TRUE){
   dr.tsne <- read.csv(paste0("./dr_tSNE.csv"),header=TRUE)
   colnames(dr.tsne)[1] <- "Cells"
   dr.tsne <- merge(x=dr.tsne,y=id,by.x="Cells",by.y="V1",all.x=TRUE)
-  if (!dir.exists("./tsne")){
-    dir.create("./tsne")
-  }
-  png(paste0("./tsne/ClusterGroup_tSNE_",opt$g,".png"),width=500,height=500,bg="white")
+  png(paste0("./",opt$g,"/tSNE.png"),width=500,height=500,bg="white")
   plot(ggplot(dr.tsne,aes_string(x="tSNE_1",y="tSNE_2",col=opt$g))+geom_point(size=2)+labs(col="ID")+theme_cowplot())
   dev.off()
 }
@@ -35,10 +37,7 @@ if (opt$u == TRUE){
   dr.umap <- read.csv(paste0("./dr_UMAP.csv"),header=TRUE)
   colnames(dr.umap)[1] <- "Cells"
   dr.umap <- merge(x=dr.umap,y=id,by.x="Cells",by.y="V1",all.x=TRUE)
-  if (!dir.exists("./umap")){
-    dir.create("./umap")
-  }
-  png(paste0("./umap/ClusterGroup_UMAP_",opt$g,".png"),width=500,height=500,bg="white")
+  png(paste0("./",opt$g,"/UMAP.png"),width=500,height=500,bg="white")
   plot(ggplot(dr.umap,aes_string(x="UMAP_1",y="UMAP_2",col=opt$g))+geom_point(size=2)+labs(col="ID")+theme_cowplot())
   dev.off()
 }
\ No newline at end of file

workflow/scrna-seq_imgen.nf

@@ -12,6 +12,9 @@ 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
@@ -37,8 +40,8 @@ groups_plotIdentGroup = file(params.groups).readLines()
 groups_plotViolinPlot = file(params.groups)
 convert = params.convert
 
-outDir = params.outDir
-logsDir = "${outDir}/Logs"
+outDir = "${params.outDir}/deriva/Seq/${params.studyIID}/application_files/${params.applicationName}"
+logsDir = "${params.outDir}/Logs"
 
 /*
 * createMatrix: extract cell/gene matrix from Seurat object
@@ -74,7 +77,6 @@ process createMatrix {
 */
 process createGroup {
     tag "${group_createGroup}"
-    publishDir "${outDir}/matrix", mode: 'copy', overwrite: true
 
     input:
     file rda_createGroup
@@ -105,7 +107,6 @@ id.into {
 */
 process renameGenes {
     tag "NCBI"
-    publishDir "${outDir}/matrix", mode: 'copy', overwrite: false
 
     input:
     file matrixRaw
@@ -147,7 +148,7 @@ matrixFinal.into {
 */
 process plotIdentGroup {
     tag "${group_plotIdentGroup}"
-    publishDir "${outDir}/png/IdentGroup", mode: 'move', overwrite: true
+    publishDir "${outDir}", mode: 'move', overwrite: true
 
     input:
     file matrix_plotIdentGroup
@@ -224,4 +225,4 @@ process plotViolinBox {
     done < groups.txt
     wait
     """
-}
+}
\ No newline at end of file

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}
+    """
+}
\ No newline at end of file