Update docs

README.md

@@ -15,24 +15,29 @@ file of aligned reads. These outputs can then be used for downstream analysis.
 
 ## Parameters
 
-- Sample: The name of the sample. This should match the sample 
-name of the fastq files.
 - Fastq: The fastq files for the sample. Regardless of the files that are
 selected, only those matching the sample name will be included.
-- Reference: Which reference genome to use. Current choices are 
-hg38 and mm10.
-- expectCells: How many cells are expected to be present. Leave at 
-the default (0) to automatically estimate. This may be manually set if
-the estimate is inaccurate.
-- Chemistry: The chemistry used to create the library. Automatic detection
-is recommended, but if the library chemistry is **3'v1** or **multiome GEX**, 
-you must set these manually.
-- Introns: Should intronic reads be counted? Recommended to 
-keep true. Note that this **must** be true to process data from single nucleus
-suspensions.
-- noBam: Should the pipeline skip generating a bam file?
-Bam file generation is recommended, but it may be skipped to reduce file 
-size output and speed up processing time.
+
+- 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".
+    - **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
+      multiome, you must set this explicitly. Possible values:
+        - "auto": auto detect
+        - "SC3Pv1": Single cell 3' v1
+        - "SC3Pv2": Single cell 3' v2
+        - "SC3Pv3": Single cell 3' v3
+        - "SC3Pv3LT": Single cell 3' v3 LT
+        - "SC3Pv3HT": Single cell 3' v3 HT
+        - "SC5P-PE": Single cell 5' paired-end
+        - "SC5P-R2": Single cell 5' R2-only
+        - "ARC-v1": GEX only from multiome
+    - introns (true/false): Whether to count intronic reads.
+    - noBam (true/false): Whether to skip bam file generation. This will save some time and space, but
+      bam files may be required for downstream analysis and/or deposition into public databases.
 
 ## Questions
 

astrocyte_pkg.yml

@@ -23,7 +23,7 @@ description: |
 
 #### New Features in Astrocyte 0.4.0 and above ####
 citation: |
-  Nextflow 22.04.5: https://www.nextflow.io/
+  Nextflow 23.04.3: https://www.nextflow.io/
   10x Genomics Cell Ranger 7.1.0: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
   
   Please acknowledge support in publications: