From 46324047db59dbb26eceeb1a5f626ff21ea69b63 Mon Sep 17 00:00:00 2001
From: Tom Whalley <whalleyt@cardiff.ac.uk>
Date: Fri, 8 Nov 2024 15:35:49 +0000
Subject: [PATCH] new configs

---
 nf-test.config        | 10 ++++++++++
 tests/nextflow.config | 46 +++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 56 insertions(+)
 create mode 100644 nf-test.config
 create mode 100644 tests/nextflow.config

diff --git a/nf-test.config b/nf-test.config
new file mode 100644
index 0000000..7711c83
--- /dev/null
+++ b/nf-test.config
@@ -0,0 +1,10 @@
+config {
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "tests/nextflow.config"
+    libDir "tests/lib"
+    profile "docker"
+    withTrace false
+    autoSort false
+    options "-dump-channels -stub-run"
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
new file mode 100644
index 0000000..2e36793
--- /dev/null
+++ b/tests/nextflow.config
@@ -0,0 +1,46 @@
+/*
+========================================================================================
+    Nextflow config file for running tests
+========================================================================================
+*/
+
+params{
+    //standardise all fastqs to fit this schema
+    pattern = "*_{1,2}.fastq.gz"
+    
+    bowtie {
+        bowtie2_index = "s3://microbial-bioin-sp3/bowtie_hg19"
+        bowtie_index_name = "hg19_1kgmaj"
+    }
+
+    kraken {
+        kraken_db = "s3://microbial-bioin-sp3/kraken_pluspf_16gb/"
+    }
+
+    afanc {
+        afanc_myco_db = "s3://microbial-bioin-sp3/Mycobacteriaciae_DB_7.0/"
+    }
+    
+    resources {
+        resource_dir = "s3://microbial-bioin-sp3/lodestone_resources"
+        refseq = "${resource_dir}/assembly_summary_refseq.txt"
+    }        
+}
+
+aws {
+    client {
+        
+            endpoint = 'https://s3.climb.ac.uk'
+            s3PathStyleAccess = true
+    }
+}
+
+
+profiles {
+    e2e {
+        params{
+            input_dir = "s3://microbial-bioin-sp3/Lodestone_Testing_1.0/E2E_MTB"
+            output_dir = "e2e_test_out"
+        }
+    }
+}