updates seurat pipeline

labs/compiled/seurat/#14_venn_diagramm.png.2021-12-22_15-06-08.log

@@ -0,0 +1,10 @@
+INFO [2021-12-22 15:06:08] $x
+INFO [2021-12-22 15:06:08] hvgs_per_dataset
+INFO [2021-12-22 15:06:08] 
+INFO [2021-12-22 15:06:08] $filename
+INFO [2021-12-22 15:06:08] [1] "#14_venn_diagramm.png"
+INFO [2021-12-22 15:06:08] 
+INFO [2021-12-22 15:06:08] $output
+INFO [2021-12-22 15:06:08] [1] TRUE
+INFO [2021-12-22 15:06:08] 
+ERROR [2021-12-22 15:06:08] Incorrect number of elements.

labs/compiled/seurat/VennDiagram.2021-12-22_15-06-31.log

@@ -0,0 +1,7 @@
+INFO [2021-12-22 15:06:31] $x
+INFO [2021-12-22 15:06:31] hvgs_per_dataset
+INFO [2021-12-22 15:06:31] 
+INFO [2021-12-22 15:06:31] $filename
+INFO [2021-12-22 15:06:31] NULL
+INFO [2021-12-22 15:06:31] 
+ERROR [2021-12-22 15:06:31] Incorrect number of elements.

labs/compiled/seurat/seurat_01_qc.Rmd

@@ -41,28 +41,18 @@ p.caption {font-size: 0.9em;font-style: italic;color: grey;margin-right: 10%;mar
 
 In this tutorial, we will run all tutorials with a set of 6 PBMC 10x datasets from 3 covid-19 patients and 3 healthy controls, the samples have been subsampled to 1500 cells per sample. They are part of the github repo and if you have cloned the repo they should be available in folder: `labs/data/covid_data_GSE149689`. Instructions on how to download them can also be found in the Precourse material.
 
-```{bash, results='hide'}
-mkdir -p data/raw
-
-# first check if the files are there
-count=$(ls -l data/raw/*.h5 | grep -v ^d | wc -l )
-echo $count
-
-# if not 4 files, fetch the files from github.
-if (("$count" <  6)); then
-  cd data/raw
-  curl -O https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/new_dataset/labs/data/covid_data_GSE149689/sub/Normal_PBMC_13.h5
-  curl -O https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/new_dataset/labs/data/covid_data_GSE149689/sub/Normal_PBMC_14.h5
-  curl -O https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/new_dataset/labs/data/covid_data_GSE149689/sub/Normal_PBMC_5.h5
-  curl -O https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/new_dataset/labs/data/covid_data_GSE149689/sub/nCoV_PBMC_15.h5
-  curl -O https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/new_dataset/labs/data/covid_data_GSE149689/sub/nCoV_PBMC_17.h5
-  curl -O https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/new_dataset/labs/data/covid_data_GSE149689/sub/nCoV_PBMC_1.h5
-  cd ../..
-fi
-
-ls -lGa data/raw
+```{r,message='hide',warning='hide',results='hold'}
+webpath <- "https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/new_dataset/labs/data/covid_data_GSE149689/sub/"
+dir.create("./data/raw",recursive = T)
+file_list <- c("Normal_PBMC_13.h5","Normal_PBMC_14.h5","Normal_PBMC_5.h5",
+               "nCoV_PBMC_15.h5","nCoV_PBMC_17.h5","nCoV_PBMC_1.h5")
+for(i in file_list){
+  download.file( url = paste0(webpath,i) , 
+                 destfile = paste0("./data/raw/",i))
+}
 ```
 
+
 With data in place, now we can start loading libraries we will use in this tutorial.
 
 ```{r, message='hide',warning='hide',results='hold'}