Merge pull request #35 from CDCgov/dev

docs: updated readme

README.md

@@ -7,10 +7,6 @@
 
 ## This project is a successor to the [C-WAP pipeline](https://github.com/CFSAN-Biostatistics/C-WAP) and is intended to process SARS-CoV-2 wastewater samples to determine relative variant abundance.  
 
-⚠️Warning⚠️ 
-
-	This pipeline has been validated for short reads. The results generated by this pipeline are not CLIA certified and should not be considered diagnostic.
-
 ## Introduction
 **CDCgov/aquascope** is a bioinformatics best-practice pipeline for early detection of SARS-COV variants of concern, sequenced throughshotgun metagenomic sequencing, from wastewater.
 
@@ -31,27 +27,12 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
 
-3. Prepare the `assets/samplesheet.csv`
-
-	- Use the `assets/test_highcoverage_samplesheet.csv` as an example
-
-	- Create custom sample sheets using the `fastq_dir_to_samplesheet.py` script
-		
-		```
-		Usage: 
-			fastq_dir_to_samplesheet.py \
-			/absolute/path/to/fastq/dir \
-   			-st <forward/reverse/unstranded> \
-   			samplesheetName.csv 
-   		```
-
-		i. FASTQ files must be paired end, following `_R1`, `_R2` naming convention.
-
-   		ii. Strandedness must be known or "unstranded". NOTE: DNASeq is by default `unstranded`, while RNASeq is usually `stranded`
+3. Prepare the `assets/samplesheet.csv`. Refer to [prepare-files] (https://cdcgov.github.io/aquascope/).
 
 4. Prepare the configuration files
 	A. `nextflow.config` is prepared with default parameters, update as needed
 	B. `test.config` is prepared with default parameters, update as needed
+	C. `cdc-dev.config` is prepared for **CDC-Users** and it has the **Rosalind** cluster configurations.
 
 5. Run the pipeline profile
     ```