diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1e13983..2d828b9 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -39,7 +39,7 @@ docker-run:
         - if: $MATRIX_NAME == "amr"
           variables:
               NF_WORKFLOW_OPTS: "-executor.$$local.memory 16GB \
-                  --fastq test_data/isolates_fastq --sample_sheet test_data/isolates_sample_sheet.csv --threads 3 --chunk_size 100000 --isolates"
+                  --fastq s3://ont-exd-int-s3-euwst1-epi2me-labs/wf-bacterial-genomes/test_data/isolates_fastq --sample_sheet test_data/isolates_sample_sheet.csv --threads 3 --chunk_size 100000 --isolates"
               NF_IGNORE_PROCESSES: "runProkka,medakaVariant,medakaVariantConsensus,makePerSampleReports"
         - if: $MATRIX_NAME == "sample-sheet"
           variables:
@@ -49,19 +49,19 @@ docker-run:
         - if: $MATRIX_NAME == "mlst"
           variables:
               NF_WORKFLOW_OPTS: "-executor.$$local.memory 16GB \
-              --fastq test_data/isolates_fastq/barcode08 --threads 3 --chunk_size 100000 --isolates"
+              --fastq s3://ont-exd-int-s3-euwst1-epi2me-labs/wf-bacterial-genomes/test_data/isolates_fastq/barcode08 --threads 3 --chunk_size 100000 --isolates"
               NF_IGNORE_PROCESSES: "runProkka,medakaVariant,medakaVariantConsensus"
         - if: $MATRIX_NAME == "barcode04"
           # isolates barcode04 only has 4 reads and flye will fail due to low coverage
           variables:
-              NF_WORKFLOW_OPTS: "--fastq test_data/isolates_fastq/barcode04 \
+              NF_WORKFLOW_OPTS: "--fastq s3://ont-exd-int-s3-euwst1-epi2me-labs/wf-bacterial-genomes/test_data/isolates_fastq/barcode04 \
                   --threads 3 --chunk_size 100000"
               NF_IGNORE_PROCESSES: "alignReads,readStats,coverStats,splitRegions,\
                   medakaConsensus,medakaNetwork,medakaVariant,medakaVariantConsensus,makeReport,runProkka,makePerSampleReports"
         - if: $MATRIX_NAME == "mixed-species"
           variables:
               NF_WORKFLOW_OPTS: "-executor.$$local.memory 16GB \
-              --fastq test_data/isolates_fastq/ --sample_sheet test_data/isolates_mixed_sample_sheet.csv --threads 3 --chunk_size 100000 --isolates"
+              --fastq s3://ont-exd-int-s3-euwst1-epi2me-labs/wf-bacterial-genomes/test_data/isolates_fastq/ --sample_sheet test_data/isolates_mixed_sample_sheet.csv --threads 3 --chunk_size 100000 --isolates"
               NF_IGNORE_PROCESSES: "runProkka,medakaVariant,medakaVariantConsensus"
         - if: $MATRIX_NAME == "reference-iso"
           variables: