fix align reads

workflow/main.nf

@@ -155,7 +155,7 @@ process alignReads {
 
   output:
     set sampleId, file('*.bam'), experimentId, replicate into mappedReads
-    file '*.srt.bam.flagstat.qc' into mappedReadsStats
+    file '*.bam.flagstat.qc' into mappedReadsStats
 
 
   script:

workflow/tests/test_map_reads.py

@@ -9,18 +9,18 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 
 @pytest.mark.pairedend_mouse
 def test_align_reads_pairedend_mouse():
-    assert os.path.exists(os.path.join(test_output_path, 'ENCLB678IDC/ENCLB678IDC.bam'))
-    aligned_reads_report = test_output_path + 'ENCLB678IDC/ENCLB678IDC.flagstat.qc'
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB122XDP/ENCLB122XDP.bam'))
+    aligned_reads_report = test_output_path + 'ENCLB122XDP/ENCLB122XDP.flagstat.qc'
     samtools_report = open(aligned_reads_report).readlines()
-    assert '72660890 + 0 in total' in samtools_report[0]
-    assert '72053925 + 0 mapped (99.16% : N/A)' in samtools_report[4]
-    assert '71501126 + 0 properly paired (98.40% : N/A)' in samtools_report[8]
+    assert '62618664 + 0 in total' in samtools_report[0]
+    assert '59858415 + 0 mapped (95.59% : N/A)' in samtools_report[4]
+    assert '59858415 + 0 mapped (95.59% : N/A)' in samtools_report[8]
 
 
 @pytest.mark.singleend_human
 def test_align_reads_singleend_human():
-    assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI/ENCLB831RUI.bam'))
-    aligned_reads_report = test_output_path + 'ENCLB831RUI/ENCLB831RUI.flagstat.qc'
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB969KTX/ENCLB969KTX.bam'))
+    aligned_reads_report = test_output_path + 'ENCLB969KTX/ENCLB969KTX.flagstat.qc'
     samtools_report = open(aligned_reads_report).readlines()
-    assert '80795025 + 0 in total' in samtools_report[0]
-    assert '80050072 + 0 mapped (99.08% : N/A)' in samtools_report[4]
+    assert '61046225 + 0 in total' in samtools_report[0]
+    assert '59599010 + 0 mapped (97.63% : N/A)' in samtools_report[4]