diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index ea98e78..0af37b5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -32,16 +32,9 @@ jobs:
           - "--perform_longread_qc false"
           - "--perform_shortread_qc false"
           - "--shortread_qc_tool fastp"
-          - "--shortread_qc_tool fastp --shortread_qc_mergepairs --shortread_qc_includeunmerged"
-          - "--shortread_qc_tool fastp --shortread_qc_mergepairs"
           - "--shortread_qc_tool adapterremoval"
-          - "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs --shortread_qc_includeunmerged"
-          - "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs"
           - "--shortread_complexityfilter_tool bbduk"
           - "--shortread_complexityfilter_tool prinseqplusplus"
-          - "--perform_runmerging"
-          - "--perform_runmerging --shortread_qc_mergepairs"
-          - "--shortread_complexityfilter false --perform_shortread_hostremoval"
 
     steps:
       - name: Check out pipeline code