Merge pull request #10 from CDCgov/issue7

Issue7: update README

README.md

@@ -121,7 +121,7 @@ end
 3. Clone this repo to your working environment:
 
    ```console
-   git clone git@git.biotech.cdc.gov:monkeypox/mpxv-assembly-nf.git
+   git clone git@github.com:CDCgov/polkapox.git
    ```
 
 4. Prepare your samples. You have two options:
@@ -136,7 +136,7 @@ CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
 5. Start running your own analysis!
 
    ```console
-   nextflow run mpxvassembly-nf/main.nf --input {SAMPLESHEET.csv OR input_directory} --outdir {OUTDIR} --fasta {REF.fa} -profile sge,singularity --kraken_db {PATH/TO/DB} --gff {ANNOTATION.gff} --workflow {WORKFLOW} --filter {true/false}
+   nextflow run polkapox/main.nf --input {SAMPLESHEET.csv OR input_directory} --outdir {OUTDIR} --fasta {REF.fa} -profile sge,singularity --kraken_db {PATH/TO/DB} --gff {ANNOTATION.gff} --workflow {WORKFLOW} --filter {true/false}
    ```
 
    **note**: If you do not provide `--fasta`, `--gff`, or `--kraken_db`, they will default to the reference and gff in the `assets` folder of this repo, and a kraken db hosted on the SciComp file system, respectively. If you do not specify `--filter` then it will default to `true`. See `nextflow.config` for details.
@@ -159,17 +159,10 @@ For use on an HPC cluster (rosalind, aspen) the workflow can be run as a job by
     module load nextflow
     ```
 
-2) Prepare file `cdc.confing` with the necessary `sge` submission parameters, add it to sub-directory [./conf/](./conf), and include it in [nextflow.config](./nextflow.config) with:  
-
-    ```groovy
-    // Load CDC config for operating on internal compute infrastructure
-    includeConfig 'conf/cdc.config'
-    ```
-
-3) Submit individual processes as jobs to the scheduler using a profile defined in `cdc.config`: for example:
+2) Point to the `cdc.config` file, which contains custom profiles for the CDC HPC clusters. Submit individual processes as jobs to the scheduler using a profile defined in `cdc.config`.  For example, to run a job on rosalind:
 
     ```consol
-    nextflow run main.nf --input {SAMPLESHEET.csv} --outdir {OUTDIR} --fasta {REF.fa} -profile sge,singularity --kraken_db {PATH/TO/DB} --gff {ANNOTATION.gff}
+    nextflow run main.nf --input {SAMPLESHEET.csv} --outdir {OUTDIR} --fasta {REF.fa} -profile rosalind,singularity --kraken_db {PATH/TO/DB} --gff {ANNOTATION.gff} -config /scicomp/reference/nextflow/configs/cdc.config
     ```
 
 ## Documentation