Merge pull request #910 from fls-bioinformatics-core/qc-pipeline-set-…

…log-dir-on-cellranger-task Set log directory for Cellranger acquisition task in QC pipeline
fls-bioinformatics-core · Nov 3, 2023 · d78b7bf · d78b7bf
2 parents 1335c5a + 1b8213c
commit d78b7bf
Showing 1 changed file with 8 additions and 4 deletions.
diff --git a/auto_process_ngs/qc/pipeline.py b/auto_process_ngs/qc/pipeline.py
@@ -737,15 +737,17 @@ def add_project(self,project,protocol,qc_dir=None,organism=None,
                     project_name,
                     qc_module_name,
                     self.params.cellranger_exe)
-                self.add_task(required_cellranger)
+                self.add_task(required_cellranger,
+                              log_dir=log_dir)
 
                 get_cellranger = Get10xPackage(
                     "%s: get information on cellranger" % project_name,
                     require_package=\
                     required_cellranger.output.require_cellranger)
                 self.add_task(get_cellranger,
                               requires=(required_cellranger,),
-                              envmodules=self.envmodules['cellranger'])
+                              envmodules=self.envmodules['cellranger'],
+                              log_dir=log_dir)
                 check_cellranger_multi_requires.append(get_cellranger)
                 qc_metadata['cellranger_version'] = \
                         get_cellranger.output.package_version
@@ -932,7 +934,8 @@ def add_cellranger_count(self,project_name,project,qc_dir,
             (project_name,qc_module_name),
             qc_module_name,
             self.params.cellranger_exe)
-        self.add_task(required_cellranger)
+        self.add_task(required_cellranger,
+                      log_dir=log_dir)
 
         get_cellranger = Get10xPackage(
             "%s: get information on 10x pipeline package (%s)" %
@@ -941,7 +944,8 @@ def add_cellranger_count(self,project_name,project,qc_dir,
             required_cellranger.output.require_cellranger)
         self.add_task(get_cellranger,
                       requires=(required_cellranger,),
-                      envmodules=self.envmodules['cellranger'])
+                      envmodules=self.envmodules['cellranger'],
+                      log_dir=log_dir)
         check_cellranger_count_requires.append(get_cellranger)
 
         # Get reference data for cellranger