diff --git a/pipelines/nextflow/subworkflows/run_busco.nf b/pipelines/nextflow/subworkflows/run_busco.nf
index 7626e9a..9f8ada7 100644
--- a/pipelines/nextflow/subworkflows/run_busco.nf
+++ b/pipelines/nextflow/subworkflows/run_busco.nf
@@ -18,7 +18,7 @@ limitations under the License.
 
 nextflow.enable.dsl=2
 
-includeConfig '../workflows/nextflow.config'
+includeConfig '../../../workflows/nextflow.config'
 includeConfig '../conf/busco.config'
 
 
diff --git a/pipelines/nextflow/subworkflows/run_ensembl_stats.nf b/pipelines/nextflow/subworkflows/run_ensembl_stats.nf
index 63088a4..7d2e5a1 100644
--- a/pipelines/nextflow/subworkflows/run_ensembl_stats.nf
+++ b/pipelines/nextflow/subworkflows/run_ensembl_stats.nf
@@ -18,7 +18,7 @@ limitations under the License.
 
 nextflow.enable.dsl=2
 
-includeConfig '../workflows/nextflow.config'
+includeConfig '../../../workflows/nextflow.config'
 
 
 /*
diff --git a/pipelines/nextflow/subworkflows/run_omark.nf b/pipelines/nextflow/subworkflows/run_omark.nf
index e820d36..c63096a 100644
--- a/pipelines/nextflow/subworkflows/run_omark.nf
+++ b/pipelines/nextflow/subworkflows/run_omark.nf
@@ -18,7 +18,7 @@ limitations under the License.
 
 nextflow.enable.dsl=2
 
-includeConfig '../workflows/nextflow.config'
+includeConfig '../../../workflows/nextflow.config'
 includeConfig '../conf/omark.config'