From 9bdf72a24cb5bc58837203cd618786db9cd6e1bb Mon Sep 17 00:00:00 2001 From: Dan Fornika Date: Thu, 23 Nov 2023 15:48:49 -0800 Subject: [PATCH] Update README --- README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 13e01d0..49a307e 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,13 @@ # alignment-variants -[![Tests](https://github.com/dfornika/alignment-variants/actions/workflows/pull_request.yml/badge.svg)](https://github.com/dfornika/alignment-variants/actions/workflows/pull_request.yml) +[![Tests](https://github.com/BCCDC-PHL/alignment-variants/actions/workflows/pull_request.yml/badge.svg)](https://github.com/BCCDC-PHL/alignment-variants/actions/workflows/pull_request.yml) A pipeline to align (map) reads against a reference genome, and call variants based on the alignment. ## Usage ``` -nextflow run dfornika/alignment-variants \ +nextflow run BCCDC-PHL/alignment-variants \ --ref /path/to/ref.fa \ --fastq_input /path/to/fastqs \ --outdir /path/to/outputs @@ -16,7 +16,7 @@ nextflow run dfornika/alignment-variants \ Including the `--collect_outputs` flag will add the `collected_fastp.csv` and `collected_qualimap_bamqc.csv` outputs, which include results for all samples collected into a single file. ``` -nextflow run dfornika/alignment-variants \ +nextflow run BCCDC-PHL/alignment-variants \ --ref /path/to/ref.fa \ --fastq_input /path/to/fastqs \ --collect_outputs \ @@ -26,7 +26,7 @@ nextflow run dfornika/alignment-variants \ An alternative filename prefix can be set for the collected outputs using the `--collected_outputs_prefix` flag: ``` -nextflow run dfornika/alignment-variants \ +nextflow run BCCDC-PHL/alignment-variants \ --ref /path/to/ref.fa \ --fastq_input /path/to/fastqs \ --collect_outputs \ @@ -39,7 +39,7 @@ nextflow run dfornika/alignment-variants \ If long reads are available, they can be included with the `--fastq_input_long` flag: ``` -nextflow run dfornika/alignment-variants \ +nextflow run BCCDC-PHL/alignment-variants \ --ref /path/to/ref.fa \ --fastq_input /path/to/fastqs \ --fastq_input_long /path/to/long_fastqs \ @@ -49,7 +49,7 @@ nextflow run dfornika/alignment-variants \ Alternatively, a `samplesheet.csv` file can be provided: ``` -nextflow run dfornika/alignment-variants \ +nextflow run BCCDC-PHL/alignment-variants \ --ref /path/to/ref.fa \ --samplesheet_input /path/to/samplesheet.csv \ --outdir /path/to/outputs