diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a26c28b..ea98e78 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -169,5 +169,5 @@ jobs:
       - name: Run pipeline with test data
         uses: Wandalen/wretry.action@v1.0.11
         with:
-          command: nextflow run ${GITHUB_WORKSPACE} -profile test_nothing,docker --run_malt --outdir ./results
+          command: nextflow run ${GITHUB_WORKSPACE} -profile test_nothing,docker --run_malt --input 'https://github.com/nf-core/test-datasets/raw/taxprofiler/samplesheet_shortreadsonly.csv' --outdir ./results
           attempt_limit: 3
diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
index 6613648..4b4952c 100644
--- a/subworkflows/local/profiling.nf
+++ b/subworkflows/local/profiling.nf
@@ -67,7 +67,6 @@ workflow PROFILING {
         // MALT: We groupTuple to have all samples in one channel for MALT as database
         // loading takes a long time, so we only want to run it once per database
         ch_input_for_malt =  ch_input_for_profiling.malt
-                                .filter { it[0]['instrument_platform'] == 'ILLUMINA' }
                                 .map {
                                     meta, reads, db_meta, db ->