Add barnyard reference

CHANGES.md

+2024-06-20
+
+Added support for barnyard reference.
+
+2024-02-01
+
+Added ability to run multiple samples at once.
+
 2023-09-14
 
 Initial version.
\ No newline at end of file

README.md

@@ -21,7 +21,7 @@ selected, only those matching the sample name will be included.
 - sample_sheet: This is a file with the following named columns:
 
     - **sample**: The name of the sample. This must match the prefix of the associated fastq files.
-    - **reference**: Which reference genome to use. This workflow currently supports the values "hg38" or "mm10".
+    - **reference**: Which reference genome to use. This workflow currently supports the values "hg38", "mm10", or "barnyard" (hg38 and mm10 combined).
     - **expectCells**: The number of cells expected from this sample. Set to "0" for auto-detection.
     - **chemistry**: The chemistry used to generate libraries. Set to "auto" for auto-detection.
       Note that if the chemistry is 3' v1 or you're analyzing GEX data alone generated from

docs/index.md

@@ -15,7 +15,7 @@ selected, only those with prefixes matching the sample name will be included.
 - sample_sheet: This is a file with the following named columns:
 
     - **sample**: The name of the sample. This must match the prefix of the associated fastq files.
-    - **reference**: Which reference genome to use. This workflow currently supports the values "hg38" or "mm10".
+    - **reference**: Which reference genome to use. This workflow currently supports the values "hg38", "mm10", or "barnyard" (hg38 and mm10 combined).
     - **expectCells**: The number of cells expected from this sample. Set to "0" for auto-detection.
     - **chemistry**: The chemistry used to generate libraries. Set to "auto" for auto-detection.
       Note that if the chemistry is 3' v1 or you're analyzing GEX data alone generated from

test_data/sample_sheet.csv

 sample,reference,expectCells,chemistry,introns,noBam
 Brain_Tumor_3p_LT,hg38,0,auto,true,true
-hgmm_100,mm10,0,auto,true,true
\ No newline at end of file
+hgmm_100,mm10,0,auto,true,true
+hgmm_100,barnyard,0,auto,true,true
\ No newline at end of file

workflow/main.nf

@@ -42,6 +42,9 @@ process cr_count {
                 case "mm10":
                     ref = file("/project/apps_database/cellranger/refdata-gex-mm10-2020-A")
                     break
+                case "barnyard":
+                    ref = file("/project/apps_database/cellranger/refdata-gex-GRCh38_and_mm10-2020-A")
+                    break
                 default:
                     ref = file(ref)
             }