Merge pull request #36 from theislab/main

Merge from main

.gitignore

@@ -7,6 +7,3 @@ testing/
 testing*
 *.pyc
 docs/build/
-test_data/
-res_gx12/
-res_gx38/

README.md

@@ -9,6 +9,14 @@
 
 Read the [documentation](https://hadge.readthedocs.io/en/latest/) and the associated [manuscript](https://www.biorxiv.org/content/10.1101/2023.07.23.550061v1)
 
+## Quickstart
+
+```bash
+git clone https://github.com/theislab/hadge.git
+sh hadge/test_data/download_data.sh
+nextflow run main.nf -profile test
+```
+
 ## Citation
 
 hadge: a comprehensive pipeline for donor deconvolution in single cell

bin/bff.R

@@ -74,8 +74,8 @@ if(as.logical(args$preprocess)){
   # Step 3: Create a vector from the barcodesl
   vector <- unlist(words)
   print("Preprocessing")
-  #counts <- Read10X(args$fileHto) 
   counts <- ProcessCountMatrix(rawCountData = args$fileHto, barcodeBlacklist = vector)
+  print("Preprocessing done")
 }else{
   print("No preprocessing")
   counts <- Read10X(args$fileHto) 
@@ -89,19 +89,6 @@ if (!is.null(args$methodsForConsensus)) {
 
 perCell_args <- args$perCellSaturation
 perCell <- ifelse(perCell_args == "null" || perCell_args == "Null", NULL, perCell_args)
-<<<<<<< HEAD
-<<<<<<< HEAD
-print("---------------------")
-print(perCell)
-print("---------------------")
-=======
-print(perCell)
-
->>>>>>> c781241 (bff re-added problematic parameter)
-=======
-print("---------------------")
-print(perCell)
-print("---------------------")
 
 if(args$methodsForConsensus=="bff_raw" || args$methodsForConsensus=="bff_cluster" || args$methodsForConsensus=="bff_raw,bff_cluster" || is.null(args$methodsForConsensus)  )
   #Only Bff in its different variations is available

bin/demuxem.py

@@ -33,6 +33,7 @@
     # load input rna data
     rna_data = sc.read_10x_mtx(args.rna_matrix_dir)
     hashing_data = sc.read_10x_mtx(args.hto_matrix_dir,gex_only=False)
+    rna = args.rna_matrix_dir
     filter = ""
     if args.filter_demuxem.lower() in ['true', 't', 'yes', 'y', '1']:
         filter = True