From 36d0bad23d4e29d28e64c90b24e3aa117eae5682 Mon Sep 17 00:00:00 2001 From: Kaisa Thorell Date: Mon, 1 Feb 2021 13:28:23 +0100 Subject: [PATCH] Remove reference to database path close #147 --- docs/source/running.rst | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/docs/source/running.rst b/docs/source/running.rst index 796ba2b..2b77170 100644 --- a/docs/source/running.rst +++ b/docs/source/running.rst @@ -36,10 +36,11 @@ machines to high-performance computing (HPC) clusters. Changing settings on the command line ------------------------------------- -When running BACTpipe, you will most likely have to modify the paths for some -parameters so that BACTpipe can find reference databases etc. Luckily, it is -possible to modify several settings for how BACTpipe operates using -configuration parameters. All changes can be added as command-line arguments +When running BACTpipe, you may want to modify +parameters to customize it for your purpose. Luckily, +it is possible to modify several settings for how BACTpipe +operates using configuration parameters. +All changes can be added as command-line arguments when running BACTpipe, e.g.:: $ nextflow run ctmrbio/BACTpipe --shovill_kmers 21,33,55,77 --reads 'path/to/reads/*_{1,2}.fastq.gz'