Update test data and sample sheet

.gitignore

@@ -3,9 +3,6 @@ workflow/images/singularity
 workflow/*.html*
 workflow/*.csv
 
-test_data/pbmc_1k*
-test_data/Brain_Tumor*
-test_data/hgmm_100*
 test_data/fastqs
 
 *.DS_Store

test_data/fetch_test_data.sh

+#!/bin/bash
+
+mkdir -p fastqs/
+
+# Fetch 200 cell GBM data
+curl -O https://cf.10xgenomics.com/samples/cell-exp/6.0.0/Brain_Tumor_3p_LT/Brain_Tumor_3p_LT_fastqs.tar
+tar -xf Brain_Tumor_3p_LT_fastqs.tar
+mv Brain_Tumor_3p_LT_fastqs/* fastqs/
+rm -r Brain_Tumor_3p_LT_fastqs
+rm Brain_Tumor_3p_LT_fastqs.tar
+
+# Fetch 2000 cell GBM data
+curl -O https://cf.10xgenomics.com/samples/cell-exp/6.0.0/Brain_Tumor_3p/Brain_Tumor_3p_fastqs.tar
+tar -xf Brain_Tumor_3p_fastqs.tar
+mv Brain_Tumor_3p_fastqs/* fastqs/
+rm -r Brain_Tumor_3p_fastqs
+rm Brain_Tumor_3p_fastqs.tar

test_data/sample_sheet.csv

+sample,cr_reference,cr_expect_cells,cr_chemistry,cr_introns,cr_create_bam,cb_expected_cells,cb_total_droplets_included,cb_fpr,qc_nCount_threshold_lo,qc_nCount_threshold_hi,qc_nFeature_threshold_lo,qc_nFeature_threshold_hi,qc_percent.mito_threshold,md_Tissue
+Brain_Tumor_3p_LT,hg38,0,auto,true,false,0,0,0.05,400,,,,,Brain
+Brain_Tumor_3p,hg38,0,auto,true,false,0,0,0.05,400,,,,,Brain
\ No newline at end of file