Merge pull request #90 from sanger-bentley-group/dev

Dev
sanger-bentley-group · Apr 24, 2023 · d98cb52 · d98cb52
2 parents 4ab2c27 + 8ae19cf
commit d98cb52
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/lib/file_utils.py b/lib/file_utils.py
@@ -34,7 +34,7 @@ def create_output_contents(final_dict):
     def write_pandas_output(content, output_filename):
         """Write a pandas dataframe to a tab-delimited text file"""
         try:
-            content.to_csv(output_filename, sep='\t', header=True, index=False, line_terminator='\n')
+            content.to_csv(output_filename, sep='\t', header=True, index=False)
         except IOError:
             print('Cannot open filename starting "{}"'.format(output_filename))
             raise
diff --git a/modules/res_alignments.nf b/modules/res_alignments.nf
@@ -50,7 +50,7 @@ process split_target_RES_seq_from_sam_file {
     file("*_*_${pair_id}*.bai")
 
     """
-
+    set +e
     samtools view -h ${bam_file} > \$(basename ${bam_file} .bam).sam
     get_targets_from_samfile.py -s \$(basename ${bam_file} .bam).sam -t ${targets_file} -i ${pair_id} -o CHECK_
     for check_sam_file in CHECK_*_${pair_id}*.sam; do