new configs

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"
+}

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"
+        }
+    }
+}