update examples

case_studies/Covid_RNA-Seq/Nextflow/README.md

@@ -1,6 +1,6 @@
 
 ## Integrating pyrpipe scripts within a workflow management system (Nextflow)
-This example shows usage of pyrpipe with Nextflow workflow management system. The example is identical to the [Snakemake example](https://github.com/urmi-21/pyrpipe/tree/master/case_studies/Covid_RNA-Seq).
+This example shows usage of pyrpipe with Nextflow workflow management system. The example is identical to the [Snakemake example](https://github.com/urmi-21/pyrpipe/tree/master/case_studies/Covid_RNA-Seq/Snakemake).
 This example downloads COVID-19 infected human RNA-Seq data from [Rother et. al.](https://www.medrxiv.org/content/10.1101/2020.06.08.20122143v1) published under accession [SRP287810](https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP287810).
 
 Uses salmon to quantify the RNA-Seq samples and compile The transcripts TPMs for exploratory analysis with [MetaOmGraph](https://github.com/urmi-21/MetaOmGraph)
@@ -16,7 +16,7 @@ The final output file of this workflow, `results_TPM.tsv`, can be directly impor
 * Activate the environment: `conda activate pyrpipe_human`
 
 ### Prepare reference data
-To install the reference data and build Salmon index, run [this file]() as 
+To install the reference data and build Salmon index, run [this file](https://github.com/urmi-21/pyrpipe/blob/master/case_studies/Covid_RNA-Seq/Snakemake/prepare_data.sh) as 
 
 `bash prepare_data.sh`