diff --git a/README.md b/README.md
index 608de13..0f67e8e 100644
--- a/README.md
+++ b/README.md
@@ -19,13 +19,15 @@ Original pipelining and code forked from the CCBR Exome-seek Pipeline [Exome-see
 [singularity](https://singularity.lbl.gov/all-releases) must be installed on the target system. Snakemake orchestrates the execution of each step in the pipeline. To guarantee the highest level of reproducibility, each step relies on versioned images from [DockerHub](https://hub.docker.com/orgs/nciccbr/repositories). Nextflow uses singularity to pull these images onto the local filesystem prior to job execution, and as so, nextflow and singularity are the only two dependencies.
 
 ## Setup
-LOGAN is installed on the Biowulf in the ccbrpipeliner module.
-Please clone this repository to your local filesystem using the following command:
+LOGAN can be used with the Nextflow pipelining software
+Please clone this repository to your local filesystem using the following command on Biowulf:
 ```bash
 # start an interactive node
 sinteractive --mem=2g --cpus-per-task=2 --gres=lscratch:200
-# load the ccbrpipeliener module
-module load ccbrpipeliner
+git clone https://github.com/CCBR/LOGAN
+module load nextflow
+##Example run 
+nextflow run /data/LOGAN//main.nf
 ```
 
 ## Usage
@@ -89,7 +91,7 @@ c130889189_TUMOR  c130889189_PBMC
 
 #### 2.  Tumor only mode
 
-No flags are required
+No addtional flags for sample sheet are required as all samples will be used to call variants
 
 #### Calling Mode
 
@@ -97,10 +99,11 @@ Adding flags determines SNV (germline and/or somatic), SV, and/or CNV calling mo
 
 `--vc`- Enables somatic SNV calling using mutect2, vardict, varscan, octopus, strelka (TN only), MUSE (TN only), and lofreq (TN only)
 
-`--germline`- Enables germline using DV
+`--germline`- Enables germline using Deepvariant
 
 `--sv`- Enables somatic SV calling using Manta, GRIDSS, and SVABA
 
+
 `--cnv`- Enables somatic CNV calling using FREEC, Sequenza, ASCAT, CNVKit, and Purple (hg19/hg38 only)
 
 
@@ -120,26 +123,22 @@ Example: `--svcallers gridss`
 ## Running LOGAN
 Example of Tumor_Normal calling mode 
 ```bash
-# copy the logan config files to your current directory
-logan init
 # preview the logan jobs that will run 
-logan run --mode local -profile ci_stub --genome hg38 --sample_sheet samplesheet.tsv --outdir out --fastq_input "*R{1,2}.fastq.gz" -preview --vc --sv --cnv
+nextflow run /data/LOGAN/main.nf --mode local -profile ci_stub --genome hg38 --sample_sheet samplesheet.tsv --outdir out --fastq_input "*R{1,2}.fastq.gz" -preview --vc --sv --cnv
 # run a stub/dryrun of the logan jobs 
-logan run --mode local -profile ci_stub --genome hg38 --sample_sheet samplesheet.tsv --outdir out --fastq_input "*R{1,2}.fastq.gz" -stub --vc --sv --cnv
+nextflow run /data/LOGAN/main.nf --mode local -profile ci_stub --genome hg38 --sample_sheet samplesheet.tsv --outdir out --fastq_input "*R{1,2}.fastq.gz" -stub --vc --sv --cnv
 # launch a logan run on slurm with the test dataset
-logan run --mode slurm -profile biowulf,slurm --genome hg38 --sample_sheet samplesheet.tsv --outdir out --fastq_input "*R{1,2}.fastq.gz" --vc --sv --cnv 
+nextflow run /data/LOGAN/main.nf --mode slurm -profile biowulf,slurm --genome hg38 --sample_sheet samplesheet.tsv --outdir out --fastq_input "*R{1,2}.fastq.gz" --vc --sv --cnv 
 ```
 
 Example of Tumor only calling mode 
 ```bash
-# copy the logan config files to your current directory
-logan init
 # preview the logan jobs that will run 
-logan run --mode local -profile ci_stub --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 -preview --vc --sv --cnv
+nextflow run /data/LOGAN/main.nf --mode local -profile ci_stub --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 -preview --vc --sv --cnv
 # run a stub/dryrun of the logan jobs 
-logan run --mode local -profile ci_stub --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 -stub --vc --sv --cnv
+nextflow run /data/LOGAN/main.nf --mode local -profile ci_stub --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 -stub --vc --sv --cnv
 # launch a logan run on slurm with the test dataset
-logan run --mode slurm -profile biowulf,slurm --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 --vc --sv --cnv
+nextflow run /data/LOGAN/main.nf --mode slurm -profile biowulf,slurm --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 --vc --sv --cnv
 ```