move log output

broadinstitute · Dec 7, 2021 · 21b16d7 · 21b16d7
1 parent 3c98c4a
commit 21b16d7
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Showing 9 changed files with 9 additions and 9 deletions.
diff --git a/0.preprocess-sites/0.prefilter-features.py b/0.preprocess-sites/0.prefilter-features.py
@@ -26,7 +26,7 @@
 from io_utils import check_if_write
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(

diff --git a/0.preprocess-sites/1.process-spots.py b/0.preprocess-sites/1.process-spots.py
@@ -59,7 +59,7 @@
 from io_utils import check_if_write, read_csvs_with_chunksize
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(

diff --git a/0.preprocess-sites/2.process-cells.py b/0.preprocess-sites/2.process-cells.py
@@ -35,7 +35,7 @@
 from io_utils import check_if_write, read_csvs_with_chunksize
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(

diff --git a/0.preprocess-sites/3.visualize-cell-summary.py b/0.preprocess-sites/3.visualize-cell-summary.py
@@ -19,7 +19,7 @@
 from io_utils import check_if_write, read_csvs_with_chunksize
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(

diff --git a/0.preprocess-sites/4.image-and-segmentation-qc.py b/0.preprocess-sites/4.image-and-segmentation-qc.py
@@ -16,7 +16,7 @@
 from io_utils import check_if_write, read_csvs_with_chunksize
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(

diff --git a/1.generate-profiles/0.merge-single-cells.py b/1.generate-profiles/0.merge-single-cells.py
@@ -23,7 +23,7 @@
 from io_utils import read_csvs_with_chunksize
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(

diff --git a/1.generate-profiles/1.aggregate.py b/1.generate-profiles/1.aggregate.py
@@ -18,7 +18,7 @@
 from io_utils import read_csvs_with_chunksize
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(

diff --git a/1.generate-profiles/2.normalize.py b/1.generate-profiles/2.normalize.py
@@ -17,7 +17,7 @@
 from io_utils import read_csvs_with_chunksize
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(

diff --git a/1.generate-profiles/3.feature-select.py b/1.generate-profiles/3.feature-select.py
@@ -17,7 +17,7 @@
 from io_utils import read_csvs_with_chunksize
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(