From f930b370562269a5ca8d1b55406c157cf2752b8b Mon Sep 17 00:00:00 2001
From: Khoroshevskyi <sasha99250@gmail.com>
Date: Wed, 2 Oct 2024 15:14:35 -0400
Subject: [PATCH] small fixes

---
 bedboss/cli.py                    | 9 +++++++--
 docs/changelog.md                 | 4 ++++
 requirements/requirements-all.txt | 4 +---
 scripts/profiling/prof.py         | 2 +-
 4 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/bedboss/cli.py b/bedboss/cli.py
index 4f94f92..5bdd924 100644
--- a/bedboss/cli.py
+++ b/bedboss/cli.py
@@ -15,7 +15,11 @@
 
 
 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
 
@@ -23,7 +27,7 @@ def create_pm(
     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
index ec65c63..5fa4f75 100644
--- 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
index 92115fb..6fdb9cb 100644
--- 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
index d7c2fe8..09758da 100644
--- 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,