Merge pull request #44 from Pioneer-Research-Labs/add-local-no-docker-config

Add local no-docker config for running pipeline without containers

Author: jhkliu42

README.md

@@ -92,6 +92,11 @@ nextflow pull Pioneer-Research-Labs/long-read-qc
 ```bash
 nextflow run Pioneer-Research-Labs/long-read-qc --samplesheet samples.csv
 ```
+- Run without Docker using your own environment (ensure all required tools are installed and in PATH):
+
+```bash
+nextflow run Pioneer-Research-Labs/long-read-qc --samplesheet samples.csv -profile local
+````
 
 - Run on AWS Batch on the Insight server with a sample sheet entitled `samples.csv` located in the same directory:
 

nextflow.config

@@ -87,6 +87,11 @@ profiles {
         cleanup = true
     }
 
+    local {
+        process.executor = 'local'
+        cleanup = true
+    }
+
     awsbatch {
         process.executor = 'awsbatch'
         process.queue = params.queue