small fixes

databio · Oct 2, 2024 · f930b37 · f930b37
1 parent 460d045
commit f930b37
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Showing 4 changed files with 13 additions and 6 deletions.
diff --git a/bedboss/cli.py b/bedboss/cli.py
@@ -15,15 +15,19 @@
 
 
 def create_pm(
-    outfolder: str, multi: bool = False, recover: bool = True, dirty: bool = False
+    outfolder: str,
+    multi: bool = False,
+    recover: bool = True,
+    dirty: bool = False,
+    pipeline_name: str = "bedboss-pipeline",
 ):
     import pypiper
 
     pm_out_folder = outfolder
     pm_out_folder = os.path.join(pm_out_folder, "pipeline_manager")
 
     pm: pypiper.PipelineManager = pypiper.PipelineManager(
-        name="bedboss-pipeline",
+        name=pipeline_name,
         outfolder=pm_out_folder,
         version=__version__,
         multi=multi,
@@ -199,6 +203,7 @@ def run_pep(
             multi=multi,
             recover=recover,
             dirty=dirty,
+            pipeline_name=pep.replace("/", "_").replace(":", "_"),
         ),
     )
 

diff --git a/docs/changelog.md b/docs/changelog.md
@@ -7,6 +7,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 - Standardization of peps using bedbase bedms schema
 - Reference validator module
 
+## Fixed
+- Pipeline failures (due to pipeline manager)
+- Failure in cleaning temp files
+
 
 # [0.4.0] - 2024-08-26
 ## Added

diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
@@ -4,9 +4,7 @@ eido>=0.2.4
 peppy>=0.40.7
 yacman>=0.8.4
 requests>=2.28.2
-piper>=v0.14.0
-# Fixed bugs in pipestat
-pipestat>=0.11.0
+piper>=v0.14.3
 bbconf>=0.7.0
 # bbconf @ git+https://github.com/databio/bbconf.git@dev#egg=bbconf
 refgenconf>=0.12.2

diff --git a/scripts/profiling/prof.py b/scripts/profiling/prof.py
@@ -9,7 +9,7 @@ def runn():
             bedbase_config="/home/bnt4me/virginia/repos/bbuploader/config_db_local.yaml",
             outfolder="/home/bnt4me/virginia/repos/bbuploader/data",
             genome="hg38",
-            input_file="/test/data/bed/hg38/GSM6732293_Con_liver-IP2.bed",
+            input_file="/home/bnt4me/virginia/repos/bedboss/test/data/bed/hg38/GSM6732293_Con_liver-IP2.bed",
             input_type="bed",
             force_overwrite=True,
             upload_pephub=True,