Merge branch 'master' into 21-software_versions

.gitlab-ci.yml

@@ -17,6 +17,10 @@ user_configuration:
 
 single_end_mouse:
   stage: single
+  only:
+    - master
+  except:
+    - branches
   script:
   - nextflow run workflow/main.nf -resume
   - pytest -m singleend
@@ -25,6 +29,10 @@ single_end_mouse:
 
 paired_end_human:
   stage: single
+  only:
+    - branches
+  except:
+    - master
   script:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
   - pytest -m pairedend
@@ -33,6 +41,10 @@ paired_end_human:
 
 single_end_diff:
   stage: multiple
+  only:
+    - branches
+  except:
+    - master
   script:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' -resume
   - pytest -m singlediff
@@ -40,6 +52,10 @@ single_end_diff:
     expire_in: 2 days
 
 paired_end_diff:
+  only:
+    - master
+  except:
+    - branches
   stage: multiple
   script:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true -resume

workflow/tests/test_annotate_peaks.py

@@ -23,7 +23,7 @@ def test_upsetplot_singleend():
 def test_annotation_singleend():
     annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.tsv'
     assert os.path.exists(annotation_file)
-    assert utils.count_lines(annotation_file) == 152840
+    assert utils.count_lines(annotation_file) == 152255
 
 
 @pytest.mark.pairedend
@@ -40,4 +40,4 @@ def test_upsetplot_pairedend():
 def test_annotation_pairedend():
     annotation_file = test_output_path + 'ENCSR729LGA.chipseeker_annotation.tsv'
     assert os.path.exists(annotation_file)
-    assert utils.count_lines(annotation_file) == 25391
+    assert utils.count_lines(annotation_file) == 25494

workflow/tests/test_call_peaks_macs.py

@@ -41,7 +41,7 @@ def test_pvalue_signal_pairedend():
 
 @pytest.mark.pairedend
 def test_peaks_xls_pairedend():
-    assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX_peak.xls'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX_peaks.xls'))
 
 
 @pytest.mark.pairedend

workflow/tests/test_diff_peaks.py

@@ -42,7 +42,7 @@ def test_diffbind_singleend_multiple_rep():
         assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC_vs_ENCSR272GNQ_diffbind.bed'))
         diffbind_file = test_output_path + 'ENCSR238SGC_vs_ENCSR272GNQ_diffbind.csv'
     assert os.path.exists(diffbind_file)
-    assert utils.count_lines(diffbind_file) == 201039
+    assert utils.count_lines(diffbind_file) == 197471
 
 
 @pytest.mark.paireddiff

workflow/tests/test_experiment_qc.py

@@ -33,42 +33,42 @@ def test_check_update_controls(design_bam):
 @pytest.mark.singleend
 def test_coverage_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'sample_mbs.npz'))
-    assert os.path.exists(os.path.join(test_output_path, 'coverage.png'))
+    assert os.path.exists(os.path.join(test_output_path, 'coverage.pdf'))
 
 
 @pytest.mark.singleend
 def test_spearman_singleend():
-    assert os.path.exists(os.path.join(test_output_path, 'heatmap_SpearmanCorr.png'))
+    assert os.path.exists(os.path.join(test_output_path, 'heatmap_SpearmanCorr.pdf'))
 
 
 @pytest.mark.singleend
 def test_pearson_singleend():
-    assert os.path.exists(os.path.join(test_output_path, 'heatmap_PearsonCorr.png'))
+    assert os.path.exists(os.path.join(test_output_path, 'heatmap_PearsonCorr.pdf'))
 
 
 @pytest.mark.singleend
 def test_fingerprint_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'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT_fingerprint.pdf'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI_fingerprint.pdf'))
 
 
 @pytest.mark.pairdend
 def test_coverage_pairedend():
     assert os.path.exists(os.path.join(test_output_path, 'sample_mbs.npz'))
-    assert os.path.exists(os.path.join(test_output_path, 'coverage.png'))
+    assert os.path.exists(os.path.join(test_output_path, 'coverage.pdf'))
 
 
 @pytest.mark.pairdend
 def test_spearman_pairedend():
-    assert os.path.exists(os.path.join(test_output_path, 'heatmap_SpearmanCorr.png'))
+    assert os.path.exists(os.path.join(test_output_path, 'heatmap_SpearmanCorr.pdf'))
 
 
 @pytest.mark.pairdend
 def test_pearson_pairedend():
-    assert os.path.exists(os.path.join(test_output_path, 'heatmap_PearsonCorr.png'))
+    assert os.path.exists(os.path.join(test_output_path, 'heatmap_PearsonCorr.pdf'))
 
 
 @pytest.mark.pairdend
 def test_fingerprint_pairedend():
-    assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX_fingerprint.png'))
-    assert os.path.exists(os.path.join(test_output_path, 'ENCLB637LZP_fingerprint.png'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX_fingerprint.pdf'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB637LZP_fingerprint.pdf'))

workflow/tests/test_map_qc.py

@@ -53,4 +53,4 @@ def test_library_complexity_pairedend():
     df_library_complexity = pd.read_csv(library_complexity, sep='\t')
     assert  df_library_complexity["NRF"].iloc[0] == 0.947064
     assert  round(df_library_complexity["PBC1"].iloc[0],6) == 0.946723
-    assert  df_library_complexity["PBC2"].iloc[0] == 18.643039
+    assert  round(df_library_complexity["PBC2"].iloc[0],6) == 18.642645

workflow/tests/test_overlap_peaks.py

@@ -37,11 +37,11 @@ def test_check_update_design(design_diff):
 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) == 152848
+    assert utils.count_lines(peak_file) == 152262
 
 
 @pytest.mark.pairedend
 def test_overlap_peaks_pairedend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.rejected.narrowPeak'))
     peak_file = test_output_path + 'ENCSR729LGA.replicated.narrowPeak'
-    assert utils.count_lines(peak_file) == 26281
+    assert utils.count_lines(peak_file) == 25758

workflow/tests/test_trim_reads.py

@@ -21,7 +21,7 @@ def test_trim_reads_singleend():
 @pytest.mark.singleend
 def test_trim_report_singleend():
     trimmed_fastq_report = test_output_path + \
-                            'ENCLB144FDT_R1_trimmed.fq.gz_trimming_report.txt'
+                            'ENCLB144FDT_R1.fastq.gz_trimming_report.txt'
     assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4]