updated kraken2 test db path

phac-nml · May 1, 2024 · 27356d8 · 27356d8
1 parent 8fc50d0
commit 27356d8
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Showing 2 changed files with 9 additions and 7 deletions.
diff --git a/tests/main.nf.test b/tests/main.nf.test
@@ -18,6 +18,8 @@ nextflow_pipeline {
 
                 dehosting_idx = "https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/databases/campy.mmi"
 
+                kraken2_db = "$baseDir/tests/data/kraken2/test"
+
                 min_reads = 100
 
                 skip_bakta = true
@@ -90,7 +92,7 @@ nextflow_pipeline {
                 mh_min_kmer = 1
 
                 dehosting_idx = "https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/databases/campy.mmi"
-                kraken2_db = "$launchDir/tests/kraken2/test"
+                kraken2_db = "$baseDir/tests/data/kraken2/test"
 
                 min_reads = 100
 
@@ -193,7 +195,7 @@ nextflow_pipeline {
                 mh_min_kmer = 1
 
                 dehosting_idx = "https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/databases/campy.mmi"
-                kraken2_db = "$launchDir/tests/kraken2/test"
+                kraken2_db = "$baseDir/tests/data/kraken2/test"
 
                 min_reads = 100
 
@@ -233,7 +235,7 @@ nextflow_pipeline {
 
                 dehosting_idx = "https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/databases/campy.mmi"
 
-                kraken2_db = "$launchDir/tests/kraken2/test"
+                kraken2_db = "$baseDir/tests/data/kraken2/test"
 
                 min_reads = 100
 
@@ -272,7 +274,7 @@ nextflow_pipeline {
 
                 dehosting_idx = "https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/databases/campy.mmi"
 
-                kraken2_db = "$launchDir/tests/kraken2/test"
+                kraken2_db = "$baseDir/tests/data/kraken2/test"
 
                 min_reads = 100
 

diff --git a/tests/pipelines/main.from_assemblies.nf.test b/tests/pipelines/main.from_assemblies.nf.test
@@ -15,7 +15,7 @@ nextflow_pipeline {
 
                 mash_sketch = "https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/databases/campy-staph-ecoli.msh"
                 dehosting_idx = "https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/databases/campy.mmi"
-                kraken2_db = "$launchDir/tests/kraken2/test"
+                kraken2_db = "$baseDir/tests/data/kraken2/test"
                 qt_min_contig_length = 1
 
                 skip_bakta = true
@@ -120,7 +120,7 @@ nextflow_pipeline {
 
                 mash_sketch = "https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/databases/mash.msh"
                 dehosting_idx = "https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/databases/campy.mmi"
-                kraken2_db = "$launchDir/tests/kraken2/test"
+                kraken2_db = "$baseDir/tests/data/kraken2/test"
                 qt_min_contig_length = 1
 
                 skip_bakta = true
@@ -246,7 +246,7 @@ nextflow_pipeline {
 
                 mash_sketch = "https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/databases/mash.msh"
                 dehosting_idx = "https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/databases/campy.mmi"
-                kraken2_db = "$launchDir/tests/kraken2/test"
+                kraken2_db = "$baseDir/tests/data/kraken2/test"
                 qt_min_contig_length = 1
 
                 skip_bakta = true