Add report_file from bioluigi 0.0.8 to cutadapt tasks (fix #47)

PavlidisLab · Feb 8, 2022 · fafd38e · fafd38e
1 parent d4771d5
commit fafd38e
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/rnaseq_pipeline/tasks.py b/rnaseq_pipeline/tasks.py
@@ -103,6 +103,7 @@ def run(self):
                     r1.path,
                     join(destdir, os.path.basename(r1.path)),
                     minimum_length=self.minimum_length,
+                    report_file=join(destdir, os.path.basename(r1.path) + '.cutadapt.json'),
                     cpus=4)
         elif len(self.input()) == 2:
             r1, r2 = self.input()
@@ -113,20 +114,23 @@ def run(self):
                         r2.path,
                         join(destdir, os.path.basename(r2.path)),
                         minimum_length=self.minimum_length,
+                        report_file=join(destdir, os.path.basename(r2.path) + '.cutadapt.json'),
                         cpus=4)
             elif self.ignore_mate == 'reverse':
                 logger.info('Reverse mate is ignored for %s.', repr(self))
                 yield platform.get_trim_single_end_reads_task(
                         r1.path,
                         join(destdir, os.path.basename(r1.path)),
                         minimum_length=self.minimum_length,
+                        report_file=join(destdir, os.path.basename(r1.path) + '.cutadapt.json'),
                         cpus=4)
             else:
                 yield platform.get_trim_paired_reads_task(
                         r1.path, r2.path,
                         join(destdir, os.path.basename(r1.path)),
                         join(destdir, os.path.basename(r2.path)),
                         minimum_length=self.minimum_length,
+                        report_file=join(destdir, os.path.basename(r1.path) + '_' + os.path.basename(r2.path) + '.cutadapt.json'),
                         cpus=4)
         else:
             raise NotImplementedError('Trimming more than two mates is not supported.')