QC_Analysis_TellReadJob.html (#139)

* QC_Analysis_TellReadJob.html

* pip freeze | grep test

* pip --version

* pip freeze

* python --version

* 3.9.21

* changing tests

* clean up

* make sure the output_dir is empty

* add prints

* some more prints

* print metadata

* more prints

* more prints

* add sorted

* key int

* clean up

Author: antgonza

src/qp_klp/Assays.py

@@ -601,8 +601,8 @@ def update_prep_templates(self):
         :return: A dict of lists of prep-ids, keyed by study-id.
         """
         results = defaultdict(list)
-
-        for study_id in self.prep_file_paths:
+        # sorting to assure order
+        for study_id in sorted(self.prep_file_paths, key=lambda x: int(x)):
             for prep_fp in self.prep_file_paths[study_id]:
                 afact_name, is_repl = self._generate_artifact_name(prep_fp)
 

src/qp_klp/Workflows.py

@@ -285,7 +285,8 @@ def _helper_process_operations(self):
 
                    (['failed_samples.html',
                      'touched_studies.html',
-                     'MultiQCJob/multiqc'],
+                     'MultiQCJob/multiqc',
+                     'TellReadJob/QC_Analysis_TellReadJob.html'],
                     'mv', RESULTS_DIR, 'INPUTS_FIRST'),
 
                    (['FastQCJob/multiqc'], 'mv', RESULTS_DIR, 'INPUTS_FIRST')]