From 7115c890832951625c757ea29301df317bbf6589 Mon Sep 17 00:00:00 2001 From: Alejandra Escobar Date: Tue, 16 Apr 2024 10:31:52 +0100 Subject: [PATCH] Test info added to README --- README.md | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 384e6f5..592c611 100644 --- a/README.md +++ b/README.md @@ -94,12 +94,18 @@ Use `--core_mode true` for large catalogues like the mouse-gut to avoid over-pre Nextflow option `-profile` can be use to select a suitable config for your computational resources. You can add profile files to the `config` directory. Nextflow option `-resume` can be use to re-run the pipeline from the last successfully finished step. - ## Test -To test the pipeline you can run... - +To test the installed tool with your douwnloaded databases you can run the pipeline using the small test dataset. Even if there are no hits with the biome you are interested, the pipeline should finish successfully. Add `-profile` if you have set up a config profile for your compute resources. +```bash +cd shallowmapping/tests +nextflow run ../main.nf \ + --input test_samplesheet.csv \ + --biome \ + --shallow_dbs_path \ + --decont_reference_paths +``` ## Credits