Change test data from gbm to pbmc

.gitignore

@@ -2,8 +2,9 @@ workflow/work
 workflow/images/singularity
 workflow/*.html*
 workflow/*.csv
+workflow/test.nf
 
-test_data/fastqs
+test_data/fastqs*
 
 *.DS_Store
 .history

test_data/fetch_test_data.sh → test_data/fetch_test_data_gbm.sh

 #!/bin/bash
 
-mkdir -p fastqs/
+mkdir -p fastqs_gbm/
 
 # 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/
+mv Brain_Tumor_3p_LT_fastqs/* fastqs_gbm/
 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/
+mv Brain_Tumor_3p_fastqs/* fastqs_gbm/
 rm -r Brain_Tumor_3p_fastqs
 rm Brain_Tumor_3p_fastqs.tar

test_data/fetch_test_data_pbmc.sh

+#!/bin/bash
+
+mkdir -p fastqs_pbmc/
+
+# Fetch PBMC donor 3
+#curl -O https://cf.10xgenomics.com/samples/cell-exp/9.0.0/5k_Human_Donor3_PBMC_3p_gem-x_Multiplex/5k_Human_Donor3_PBMC_3p_gem-x_Multiplex_fastqs.tar
+tar -xf 5k_Human_Donor3_PBMC_3p_gem-x_Multiplex_fastqs.tar
+mv 5k_Human_Donor3_PBMC_3p_gem-x_GEX_fastqs/* fastqs_pbmc/
+rm -r 5k_Human_Donor3_PBMC_3p_gem-x_GEX_fastqs
+rm 5k_Human_Donor3_PBMC_3p_gem-x_Multiplex_fastqs.tar
+
+# Fetch PBMC donor 4
+#curl -O https://cf.10xgenomics.com/samples/cell-exp/9.0.0/5k_Human_Donor4_PBMC_3p_gem-x_Multiplex/5k_Human_Donor4_PBMC_3p_gem-x_Multiplex_fastqs.tar
+tar -xf 5k_Human_Donor4_PBMC_3p_gem-x_Multiplex_fastqs.tar
+mv 5k_Human_Donor4_PBMC_3p_gem-x_GEX_fastqs/* fastqs_pbmc/
+rm -r 5k_Human_Donor4_PBMC_3p_gem-x_GEX_fastqs
+rm 5k_Human_Donor4_PBMC_3p_gem-x_Multiplex_fastqs.tar

test_data/sample_sheet_pbmc.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
+5k_Human_Donor3_PBMC_3p_gem-x_GEX,hg38,0,auto,true,false,0,0,0.05,400,,,,,PBMC
+5k_Human_Donor4_PBMC_3p_gem-x_GEX,hg38,0,auto,true,false,0,0,0.05,400,,,,,PBMC