Merge pull request #43 from Pathogen-Genomics-Cymru/climb

CLIMB profile
Pathogen-Genomics-Cymru · Oct 18, 2023 · 0d28771 · 0d28771
2 parents c1e1523 + 5543209
commit 0d28771
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diff --git 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
 

diff --git 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'