diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9aebbdae91e62cba7b759e7e9b9fc4cda2a9cd6b..7542f3cd4a72c01ad8ebc04a6fa74983f772c858 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -7,7 +7,6 @@ before_script:
 stages:
   - unit
   - integration
-  - acceptance
 
 user_configuration:
   stage: unit
@@ -18,8 +17,4 @@ single_end_mouse:
   stage: integration
   script:
   - nextflow run workflow/main.nf
-
-single_end_acceptance:
-  stage: acceptance
-  script:
-  - pytest -m acceptance
+  - pytest -m integration
diff --git a/workflow/tests/test_call_peaks_macs.py b/workflow/tests/test_call_peaks_macs.py
index 62ec2e3bd2f931e44d746d917f2396b0d0494575..6182f24ed407eac85dcbaf155272b6f67b6b3a5a 100644
--- a/workflow/tests/test_call_peaks_macs.py
+++ b/workflow/tests/test_call_peaks_macs.py
@@ -8,7 +8,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/callPeaksMACS/'
 
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_call_peaks_macs_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.fc_signal.bw'))
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.pvalue_signal.bw'))
@@ -16,7 +16,7 @@ def test_call_peaks_macs_singleend():
     assert utils.count_lines(peak_file) == 210349
 
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_call_peaks_macs_pairedend():
     # Do the same thing for paired end data
     pass
diff --git a/workflow/tests/test_convert_reads.py b/workflow/tests/test_convert_reads.py
index bae2ff242a340dcb37c3bc5a5eec34470a69b485..1067547943b54cce1d4ae2cf10f03517f342c2bd 100644
--- a/workflow/tests/test_convert_reads.py
+++ b/workflow/tests/test_convert_reads.py
@@ -7,7 +7,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/convertReads/'
 
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_convert_reads_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.tagAlign.gz'))
     assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bedse.gz'))
diff --git a/workflow/tests/test_experiment_design.py b/workflow/tests/test_experiment_design.py
index 7dca74ce10e4d8b3e4c7c3b9dac8f38cd23b8ad4..51ada8680d4f5d74881715f64ad7137301ea592f 100644
--- a/workflow/tests/test_experiment_design.py
+++ b/workflow/tests/test_experiment_design.py
@@ -30,7 +30,7 @@ def test_check_update_controls_tag(design_tag):
     assert new_design.loc[0, 'control_tag_align'] == "B_1.tagAlign.gz"
 
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_experiment_design_single_end():
     design_file = os.path.join(test_output_path, 'ENCSR238SGC.tsv')
     assert os.path.exists(design_file)
@@ -38,7 +38,7 @@ def test_experiment_design_single_end():
     assert design_df.shape[0] == 2
 
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_experiment_design_paired_end():
     # Do the same thing for paired end data
     pass
diff --git a/workflow/tests/test_experiment_qc.py b/workflow/tests/test_experiment_qc.py
index d9ab346526bf0c268431e01ea0897ae38adeb11f..875aea6e4d955de53347b848705ffd5581752c23 100644
--- a/workflow/tests/test_experiment_qc.py
+++ b/workflow/tests/test_experiment_qc.py
@@ -30,7 +30,7 @@ def test_check_update_controls(design_bam):
     assert new_design.loc[0, 'control_reads'] == "B_1.bam"
 
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_experiment_qc_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'sample_mbs.npz'))
     assert os.path.exists(os.path.join(test_output_path, 'heatmap_SpearmanCorr.png'))
@@ -38,7 +38,7 @@ def test_experiment_qc_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT_fingerprint.png'))
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI_fingerprint.png'))
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_experiment_qc_pairedend():
     # Do the same thing for paired end data
     pass
diff --git a/workflow/tests/test_map_qc.py b/workflow/tests/test_map_qc.py
index 9255e20e2fedefa108f62030363a7e6fb0be3097..a882e53a0fc45ee9fa9d501b5160e73ebd2816c5 100644
--- a/workflow/tests/test_map_qc.py
+++ b/workflow/tests/test_map_qc.py
@@ -8,7 +8,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/filterReads/'
 
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_map_qc_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bam'))
     assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bam.bai'))
@@ -23,6 +23,7 @@ def test_map_qc_singleend():
     assert  df_library_complexity["PBC2"].iloc[0] == 13.706885
 
 
+@pytest.mark.integration
 def test_map_qc_pairedend():
     # Do the same thing for paired end data
     pass
diff --git a/workflow/tests/test_map_reads.py b/workflow/tests/test_map_reads.py
index 1bcf609c7f72262bd4c030935fcc7aa7936a5fcb..5c2ff2be2e5ec0e3675ea3713790743fc3aff344 100644
--- a/workflow/tests/test_map_reads.py
+++ b/workflow/tests/test_map_reads.py
@@ -7,7 +7,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/alignReads/'
 
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_map_reads_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.srt.bam'))
     aligned_reads_report = test_output_path + 'ENCFF646LXU.srt.bam.flagstat.qc'
@@ -16,7 +16,7 @@ def test_map_reads_singleend():
     assert '80050072 + 0 mapped (99.08% : N/A)' in samtools_report[4]
 
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_map_reads_pairedend():
     # Do the same thing for paired end data
     pass
diff --git a/workflow/tests/test_overlap_peaks.py b/workflow/tests/test_overlap_peaks.py
index 52fa0e5bc6c5b5b1d78aad9eb224f762239ab604..f75ebcd43d45c18b1418aab0c7340122e2a8ff06 100644
--- a/workflow/tests/test_overlap_peaks.py
+++ b/workflow/tests/test_overlap_peaks.py
@@ -33,14 +33,14 @@ def test_check_update_design(design_diff):
     assert new_design.loc[0, 'peak_caller'] == "bed"
 
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_overlap_peaks_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.rejected.narrowPeak'))
     peak_file = test_output_path + 'ENCSR238SGC.replicated.narrowPeak'
     assert utils.count_lines(peak_file) == 150302
 
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_call_peaks_macs_pairedend():
     # Do the same thing for paired end data
     pass
diff --git a/workflow/tests/test_pool_and_psuedoreplicate.py b/workflow/tests/test_pool_and_psuedoreplicate.py
index de6f94e99830c10d33250b5398966e025bdaab29..6c30f7e1bb5bbaf3aa21b46bc3e54c1f0e162163 100644
--- a/workflow/tests/test_pool_and_psuedoreplicate.py
+++ b/workflow/tests/test_pool_and_psuedoreplicate.py
@@ -60,7 +60,7 @@ def test_check_controls_single(design_experiment_3):
     assert no_controls == 1
 
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_pool_and_psuedoreplicate_single_end():
     design_file = os.path.join(test_output_path, 'ENCSR238SGC_ppr.tsv')
     assert os.path.exists(design_file)
@@ -68,7 +68,7 @@ def test_pool_and_psuedoreplicate_single_end():
     assert design_df.shape[0] == 5
 
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_experiment_design_paired_end():
     # Do the same thing for paired end data
     pass
diff --git a/workflow/tests/test_trim_reads.py b/workflow/tests/test_trim_reads.py
index ad90935081333c1dc48559414a5ee8f32bd3f121..92f4716b21ac7ad3cde599ee08edf34f095e70e6 100644
--- a/workflow/tests/test_trim_reads.py
+++ b/workflow/tests/test_trim_reads.py
@@ -10,7 +10,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 
 
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_trim_reads_singleend():
     raw_fastq = test_data_path + 'ENCFF833BLU.fastq.gz'
     trimmed_fastq = test_output_path + 'ENCFF833BLU_trimmed.fq.gz'
@@ -21,7 +21,7 @@ def test_trim_reads_singleend():
     assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4]
 
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_trim_reads_pairedend():
     # Do the same thing for paired end data
     pass
diff --git a/workflow/tests/test_xcor.py b/workflow/tests/test_xcor.py
index d1ccead9ac2d5ec54c1e30b8e65d33298e01f454..cf4840850e4b236e853882a3820e456259c7b17a 100644
--- a/workflow/tests/test_xcor.py
+++ b/workflow/tests/test_xcor.py
@@ -8,7 +8,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/crossReads/'
 
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_convert_reads_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCFF833BLU.filt.nodup.tagAlign.15.tagAlign.gz.cc.plot.pdf'))
     qc_file = os.path.join(test_output_path,"ENCFF833BLU.filt.nodup.tagAlign.15.tagAlign.gz.cc.qc")
@@ -18,7 +18,7 @@ def test_convert_reads_singleend():
     assert df_xcor[9].iloc[0] == 1.266678
 
 
-@pytest.mark.acceptance
+@pytest.mark.integration
 def test_map_qc_pairedend():
     # Do the same thing for paired end data
     pass