From 46bfeabeb802f966f4efd3f08b1e1685ccdda223 Mon Sep 17 00:00:00 2001 From: "Diego Alvarez S." Date: Wed, 4 Sep 2024 22:31:11 -0300 Subject: [PATCH] Update README --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ad8e8d5..fbf6b54 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # ONT Basecalling / Demux Pipeline -Small pipeline to perform basecalling and (optional) demultiplexing of ONT data, collect QC metrics and generate a MultiQC report. +Nextflow pipeline to perform basecalling and (optional) demultiplexing of ONT data, collect QC metrics and generate a MultiQC report. Uses Dorado for basecalling and demultiplexing. ## Requirements @@ -35,7 +35,7 @@ Uses Dorado for basecalling and demultiplexing. | `experiment_name` | No | - | Name of the experiment, used for final reports (title and filename). | | `data_dir` | Yes | - | Path to the directory containing POD5 files. | | `sample_data` | No | - | Path to the CSV file containing the sample data (if not provided, will not perform demux). | -| `output_dir` | No | `demultiplex_results` | Directory for saving results. | +| `output_dir` | No | `results` | Directory for saving results. | | `fastq_output` | No | `true` | Generates FASTQ files if `true`; otherwise, generates UBAM files. | | `qscore_filter` | No | `10` | Minimum QScore threshold for "pass" data, used in demultiplexing. | | `dorado_basecalling_model` | No | `sup` | Model used for basecalling. Check Dorado help for available options. |