From 30ac0cd71c41a3e70f6a56d5213364a7b34fbb63 Mon Sep 17 00:00:00 2001 From: whalleyt Date: Wed, 18 Oct 2023 09:52:03 +0000 Subject: [PATCH 1/2] climb profile --- nextflow.config | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/nextflow.config b/nextflow.config index 4f53070..b023a89 100644 --- a/nextflow.config +++ b/nextflow.config @@ -55,6 +55,15 @@ params { } profiles { + climb { + params{ + bowtie2_index = "/shared-team/db/bowtie2/hg19" + bowtie_index_name = "hg19_1kgmaj" + kraken_db = "/shared-team/db/kraken2/pluspf_16" + afanc_myco_db = "/shared-team/db/afanc/Mycobacteriaciae_DB_7.0" + + } + } singularity { singularity.enabled = 'true' From 55432098d4d54ce6a83feab805a80c4fd6b55d32 Mon Sep 17 00:00:00 2001 From: whalleyt Date: Wed, 18 Oct 2023 09:58:42 +0000 Subject: [PATCH 2/2] readme update --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index f14831d..38f39c7 100644 --- a/README.md +++ b/README.md @@ -127,6 +127,9 @@ process clockwork:alignToRef\ process clockwork:minos\ 26. (Warn) If sample is not TB, then it is not passed to gnomonicus +## Running on CLIMB Jupyter Hub +There is a pre-configured climb profile to run Lodestone on a CLIMB Jupyter Notebook Server. Add ```profile climb,docker``` your command invocation. The input directory can point to an S3 bucket natively (e.g. ```--input_dir s3://my-team/bucket```). + ## Acknowledgements ## For a list of direct authors of this pipeline, please see the contributors list. All of the software dependencies of this pipeline are recorded in the version.json