Adding detail to README and illustrating multiple fastq's in the inpu…

…t json

README.md

@@ -2,13 +2,26 @@
 # ww-star-deseq2
 [![Project Status: Experimental – Useable, some support, not open to feedback, unstable API.](https://getwilds.org/badges/badges/experimental.svg)](https://getwilds.org/badges/#experimental)
 
-This WILDS WDL workflow performs alignment using the [two-pass methodology](https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf) of [STAR](https://github.com/alexdobin/STAR) and subsequently analyzes that alignment via [DESeq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html). It is intended to be a relatively simplistic demonstration of an RNA sequencing pipeline within the context of the WILDS ecosystem.
+This WILDS WDL workflow performs alignment using the [two-pass methodology](https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf) of [STAR](https://github.com/alexdobin/STAR) and subsequently analyzes that alignment via [DESeq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html). It is intended to be a relatively straightforward demonstration of an RNA sequencing pipeline within the context of the WILDS ecosystem.
 
-## Usage
+## Basic Usage
 
-For Fred Hutch users that are new to WDL, we recommend using [PROOF](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/) to submit this workflow directly to the on-premise HPC cluster, as it simplifies interaction with Cromwell and provides a user-friendly front-end for job submission and tracking. For users outside of Fred Hutch or more advanced users who who would like to run the workflow locally, command line execution is relatively straightforward: 
+For Fred Hutch users that are new to WDL, we recommend using [PROOF](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/) to submit this workflow directly to the on-premise HPC cluster, as it simplifies interaction with Cromwell and provides a user-friendly front-end for job submission and tracking. To do this:
+
+1. Start by cloning/downloading a copy of this repository to your local machine (click "Code", then click "Download ZIP").
+2. Update [`ww-star-deseq2-inputs.json`](https://github.com/getwilds/ww-star-deseq2/blob/main/ww-star-deseq2-inputs.json) with your sample names (`omics_sample_name`) and FASTQ file paths (`R1` and `R2`).
+3. Update [`ww-star-deseq2-options.json`](https://github.com/getwilds/ww-star-deseq2/blob/main/ww-star-deseq2-inputs.json) with your preferred location for output data to be saved to (see `final_workflow_outputs_dir` field).
+4. Submit the WDL file along with your custom json's to the Fred Hutch cluster via PROOF by following our [SciWiki documentation](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/).
+
+Additional Notes:
+- Keep in mind that all file paths in the jsons must be visible to the Fred Hutch cluster, e.g. `/fh/fast/`, AWS S3 bucket. Input file paths on your local machine won't work in PROOF.
+- Specific reference genome files can be provided as inputs, but if none are provided, the workflow will automatically download a GRCh38 reference genome and use that. For the first go-around, we recommend starting with the default reference files.
+
+## Advanced Usage
+
+For users outside of Fred Hutch or more advanced users who would like to run the workflow locally, command line execution is relatively straightforward: 
 ```
-java -jar cromwell-86.jar run ww-star-deseq2.wdl --inputs ww-star-deseq2-inputs.json
+java -jar cromwell-86.jar run ww-star-deseq2.wdl --inputs ww-star-deseq2-inputs.json --options ww-star-deseq2-options.json
 ```
 Although Cromwell is demonstrated here, this pipeline is not specific to Cromwell and can be run using whichever WDL execution method you prefer ([miniwdl](https://github.com/chanzuckerberg/miniwdl), [Terra](https://terra.bio/), [HealthOmics](https://docs.aws.amazon.com/omics/latest/dev/workflows.html), etc.).
 

ww-star-deseq2-inputs.json

@@ -2,8 +2,13 @@
   "STAR2Pass.samples": [
     {
       "omics_sample_name": "SRR10724344",
-      "R1": "/path_to_input_data/SRR10724344_1.fastq.gz",
-      "R2": "/path_to_input_data/SRR10724344_2.fastq.gz"
+      "R1": "/path_to_first_input/SRR10724344_1.fastq.gz",
+      "R2": "/path_to_first_input/SRR10724344_2.fastq.gz"
+    },
+    {
+      "omics_sample_name": "SRR12345678",
+      "R1": "/path_to_second_input/SRR12345678_1.fastq.gz",
+      "R2": "/path_to_second_input/SRR12345678_2.fastq.gz"
     }
   ]
 }