Change fastq's to be new sample names as defined by the sample_id.

workflow/main.nf

@@ -104,12 +104,12 @@ process trimReads {
 
   if (pairedEnd) {
     """
-    python3 $baseDir/scripts/trim_reads.py -f ${reads[0]} ${reads[1]} -p
+    python3 $baseDir/scripts/trim_reads.py -f ${reads[0]} ${reads[1]} -s $sampleId -p
     """
   }
   else {
     """
-    python3 $baseDir/scripts/trim_reads.py -f ${reads[0]}
+    python3 $baseDir/scripts/trim_reads.py -f ${reads[0]} -s $sampleId
     """
   }
 

workflow/scripts/trim_reads.py

@@ -5,6 +5,7 @@
 import subprocess
 import argparse
 import shutil
+import os
 import logging
 
 EPILOG = '''
@@ -32,6 +33,10 @@ def get_args():
                         nargs='+',
                         required=True)
 
+    parser.add_argument('-s', '--sample',
+                        help="The name of the sample.",
+                        required=True)
+
     parser.add_argument('-p', '--paired',
                         help="True/False if paired-end or single end.",
                         default=False,
@@ -61,6 +66,32 @@ def check_tools():
         raise Exception('Missing cutadapt')
 
 
+def rename_reads(fastq, sample, paired):
+    '''Rename fastq files by sample name.'''
+
+    # Get current directory to build paths
+    cwd = os.getcwd()
+
+    renamed_fastq = []
+
+    if paired:  # paired-end data
+        # Set file names
+        renamed_fastq[0] = cwd + '/' + sample + '_R1.fastq.gz'
+        renamed_fastq[1] = 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[0] = cwd + '/' + sample + '_R1.fastq.gz'
+
+        # Great symbolic links
+        os.symlink(fastq[0], renamed_fastq[0])
+
+    return fastq_rename
+
+
 def trim_reads(fastq, paired):
     '''Run trim_galore on 1 or 2 files.'''
 
@@ -82,6 +113,7 @@ def trim_reads(fastq, paired):
 def main():
     args = get_args()
     fastq = args.fastq
+    sample = args.sample
     paired = args.paired
 
     # Create a file handler
@@ -91,8 +123,11 @@ def main():
     # Check if tools are present
     check_tools()
 
+    # Rename fastq files by sample
+    fastq_rename = rename_reads(fastq, sample paired)
+
     # Run trim_reads
-    trim_reads(fastq, paired)
+    trim_reads(fastq_rename, paired)
 
 
 if __name__ == '__main__':

workflow/tests/test_trim_reads.py

@@ -13,9 +13,9 @@ 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 + 'ENCFF833BLU_trimmed.fq.gz'
+    trimmed_fastq = test_output_path + 'ENCLB144FDT_trimmed.fq.gz'
     trimmed_fastq_report = test_output_path + \
-                            'ENCFF833BLU.fastq.gz_trimming_report.txt'
+                            'ENCLB144FDT.fastq.gz_trimming_report.txt'
     assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
     assert os.path.getsize(trimmed_fastq) == 2512853101
     assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4]
@@ -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 + ' ENCFF582IOZ_val_2.fq.gz'
+    trimmed_fastq = test_output_path + ' ENCLB637LZP_val_2.fq.gz'
     trimmed_fastq_report = test_output_path + \
-                            'ENCFF582IOZ.fastq.gz_trimming_report.txt'
+                            'ENCLB637LZP.fastq.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]