Improve RESUME scripts

Author: cakirb

examples/RESUME-scautoqc-all1

@@ -10,6 +10,9 @@ nextflow run cellgeni/nf-scautoqc -r main \
   --metadata /path/to/metadata/file \
   --ss_prefix /path/to/starsolo-results \
   --cb_prefix /path/to/cellbender-results \
+  --cell_or_nuclei cell \
+  --cellbender_input cellbender_out_filtered.h5 \
+  --celltypist gut \
   --ss_out Gene \
   --project_tag project1 \
   --batch_key sampleID \

examples/RESUME-scautoqc-all2

@@ -8,6 +8,9 @@ nextflow run cellgeni/nf-scautoqc -r main \
   -entry all \
   --SAMPLEFILE /path/to/sample/file \
   --metadata /path/to/metadata/file \
+  --qc_mode original \
+  --cellbender_input cellbender_out_filtered.h5 \
+  --celltypist gut \
   --ss_out Gene \
   --project_tag project1 \
   --batch_key sampleID \

examples/RESUME-scautoqc-onlyqc

@@ -7,6 +7,10 @@ nextflow run cellgeni/nf-scautoqc -r main \
   --SAMPLEFILE /path/to/sample/file \
   --ss_prefix /path/to/starsolo-results \
   --cb_prefix /path/to/cellbender-results \
+  --qc_mode original \
+  --cell_or_nuclei cell \
+  --cellbender_input cellbender_out_filtered.h5 \
+  --celltypist gut \
   --ss_out Gene \
   --project_tag project1 \
   --batch_key sampleID \

resume/RESUME-scautoqc-all

@@ -10,6 +10,9 @@ nextflow run cellgeni/nf-scautoqc -r main \
   --metadata /path/to/metadata/file \
   --ss_prefix /path/to/starsolo-results \
   --cb_prefix /path/to/cellbender-results \
+  --cell_or_nuclei cell \
+  --cellbender_input cellbender_out_filtered.h5 \
+  --celltypist gut \
   --ss_out Gene \
   --project_tag project1 \
   --batch_key sampleID \