update README.md

Author: YanyanLiuBio

README.md

@@ -58,6 +58,9 @@ Path to a directory containing FASTQ files generated by Dorado high-accuracy bas
 #### `--outdir`
 The output directory path where results will be saved. This can be a local absolute path or an AWS S3 URI. If using an AWS S3 URI, please ensure your security credentials are configured in the `nextflow.config` file.
 
+#### `--pool_ID`
+A unique identifier for the ONT sequencing run being demultiplexed.
+
 #### `--barcodes`
 Path to the barcode FASTA file used for Dorado demultiplexing. The default barcode file (**barcodes.384.fa**) is located in the `assets` folder.
 
@@ -80,6 +83,7 @@ nextflow run \
     main.nf \
     --input "${PWD}/path/to/fastq/directory" \
     --outdir "${PWD}/path/to/output" \
+    --pool_ID "test" \
     -resume -bg
 ```
 
@@ -92,6 +96,7 @@ nextflow run \
     main.nf \
     --input "${PWD}/test_data/fastq_pass" \
     --outdir "${PWD}/test_output" \
+    --pool_ID "384_test" \
     -resume -bg
 ```
 

nextflow.config

@@ -34,7 +34,7 @@ profiles {
     process.executor = 'local'
     docker.enabled = true
     params {
-      input = "test_data/fastq_pass"          // Path to input FASTQ file(s), e.g. --input "fastq_pass"
+      input = "test_data/fastq_pass/*.fastq.gz"          // Path to input FASTQ file(s)
       barcodes = "assets/barcodes.384.fa"        // Path to barcode file, e.g. --barcodes barcode.fa
       arrangement_toml = "assets/arrangement.toml"
       outdir = 'ci_output'                    // Default output directory