Fix Trim reads output to match.

workflow/scripts/trim_reads.py

@@ -76,15 +76,15 @@ def rename_reads(fastq, sample, paired):
 
     if paired:  # paired-end data
         # Set file names
-        renamed_fastq.append(cwd + '/' + sample + '_R1.fq.gz')
-        renamed_fastq.append(cwd + '/' + sample + '_R2.fq.gz')
+        renamed_fastq.append(cwd + '/' + sample + '_R1.fastq.gz')
+        renamed_fastq.append(cwd + '/' + sample + '_R2.fastq.gz')
 
         # Great symbolic links
         os.symlink(fastq[0], renamed_fastq[0])
         os.symlink(fastq[1], renamed_fastq[1])
     else:
         # Set file names
-        renamed_fastq.append(cwd + '/' + sample + '_R1.fq.gz')
+        renamed_fastq.append(cwd + '/' + sample + '_R1.fastq.gz')
 
         # Great symbolic links
         os.symlink(fastq[0], renamed_fastq[0])

workflow/tests/test_trim_reads.py

@@ -13,7 +13,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 @pytest.mark.singleend
 def test_trim_reads_singleend():
     raw_fastq = test_data_path + 'ENCFF833BLU.fastq.gz'
-    trimmed_fastq = test_output_path + 'ENCLB144FDT_R1_trimmed.fq.gz'
+    trimmed_fastq = test_output_path + 'ENCLB144FDT_R1.fq.gz'
     trimmed_fastq_report = test_output_path + \
                             'ENCLB144FDT_R1_trimmed.fq.gz_trimming_report.txt'
     assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
@@ -24,9 +24,9 @@ def test_trim_reads_singleend():
 @pytest.mark.pairedend
 def test_trim_reads_pairedend():
     raw_fastq = test_data_path + 'ENCFF582IOZ.fastq.gz'
-    trimmed_fastq = test_output_path + 'ENCLB637LZP_R2_trimmed.fq.gz'
+    trimmed_fastq = test_output_path + 'ENCLB637LZP_R2.fq.gz'
     trimmed_fastq_report = test_output_path + \
-                            'ENCLB637LZP_R2_trimmed.fq.gz_trimming_report.txt'
+                            'ENCLB637LZP_R2_val_2.fq.gz_trimming_report.txt'
     assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
     assert os.path.getsize(trimmed_fastq) == 2229312710
     assert 'Trimming mode: paired-end' in open(trimmed_fastq_report).readlines()[4]