Updated readme and examples

Author: wflynny

README.md

@@ -17,8 +17,6 @@ Fully supported
 - Multiome (joint GEX & ATAC)
 - CITE-seq with Biolegend TotalSeq-A/B/C ADTs
 - Multiplexing with BioLegend TotalSeq-A/C HTOs
-
-In progress
 - Spatial Transcriptomics (Fresh frozen and FFPE)
 - Multiplexing with CellPlex
 
@@ -86,6 +84,8 @@ TotalSeq (to specify which tags/oligos are in use) or Visium to specify image
 and probeset paths.  For now, just look in `modules/assay-type.nf` to see what
 cli options are utilized.
 
+Check out the example samplesheets under the `examples` directory.
+
 ### Things not to do:
 -   No YAML multipage documents
 
@@ -112,6 +112,7 @@ cli options are utilized.
 | | 6.0.1 | |
 | | 6.0.2 | |
 | | 6.1.1 | |
+| | 7.0.0 | |
 | CellRanger ATAC | 1.1.0 | do not use, barcode doublet issue |
 | | 1.2.0 | |
 | | 2.0.0 | |
@@ -123,6 +124,7 @@ cli options are utilized.
 | | 1.2.0 | |
 | | 1.2.2 | |
 | | 1.3.0 | |
+| | 2.0.0 | |
 
 ## Testing
 

examples/biolegend.yml

@@ -0,0 +1,2 @@
+- {libraries: [SC2200111], sample_name: my-gex-lib, library_types: [Gene Expression], tool: cellranger, tool_version: 6.1.2, command: count, is_nuclei: false, reference_path: /path/to/10x-rna/refdata-gex-GRCh38-2020-A, fastq_paths: [path/to/fastq/files], n_cells: 15000}
+- {libraries: [SC2200222], sample_name: my-hto-lib, library_types: [TotalSeq-A], tool: citeseq-count, tool_version: 1.4.5, command: , fastq_paths: [/path/to/fastq/files], tags: ["A0251", "A0252", "A0253", "A0254", "A0255", "A0256"], n_cells: 30000}

examples/visium.yml

@@ -0,0 +1,2 @@
+- { libraries: [SC2200581], sample_name: frozen-visium,  library_types: [Spatial Gene Expression], slide: V12A34-567, area: A1, image: /path/to/brightfield/image.tiff, roi_json: /path/to/image/metadata.json, tool: spaceranger, tool_version: 1.3.1, command: count, reference_path: /path/to/10x-rna/refdata-gex-mm10-2020-A, fastq_paths: [/path/to/fastq/files]}
+- { libraries: [SC2200682], sample_name: ffpe-visium, library_types: [Spatial Gene Expression], slide: V12X23-345, area: D1, image: path/to/brightfield/image.tiff, roi_json: /path/to/image/metadata.json, tool: spaceranger, tool_version: 1.3.1, command: count, probe_set: 1.3.0/Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38-2020-A.csv, reference_path: /path/to/10x-rna/refdata-gex-GRCh38-2020-A, fastq_paths: [/path/to/fastq/files]}