Merge pull request #125 from databio/dev

Release 0.7.3

Author: khoroshevskyi

bedboss/_version.py

@@ -1 +1 @@
-__version__ = "0.7.2"
+__version__ = "0.7.3"

bedboss/bedboss.py

@@ -489,6 +489,8 @@ def reprocess_all(
     """
     Run bedboss pipeline for all unprocessed beds in the bedbase
 
+    Currently only beds with genomes hg19, hg38, and mm10 are processed.
+
     :param bedbase_config: bedbase configuration file path
     :param output_folder: output folder of the pipeline
     :param limit: limit of the number of beds to process
@@ -520,7 +522,9 @@ def reprocess_all(
     else:
         raise BedBossException("Incorrect bedbase_config type. Exiting...")
 
-    unprocessed_beds = bbagent.bed.get_unprocessed(limit=limit)
+    unprocessed_beds = bbagent.bed.get_unprocessed(
+        limit=limit, genome=["hg38", "hg19", "mm10"]
+    )
 
     bbclient = BBClient()
     failed_samples = []

bedboss/cli.py

@@ -232,7 +232,9 @@ def run_pep(
     pm.stop_pipeline()
 
 
-@app.command(help="Run unprocessed files, or reprocess them")
+@app.command(
+    help="Run unprocessed files or reprocess them. Currently, only hg38, hg19, and mm10 genomes are supported."
+)
 def reprocess_all(
     bedbase_config: str = typer.Option(
         ...,

docs/changelog.md

@@ -2,6 +2,12 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+
+# [0.7.3] - 2025-06-28
+## Added:
+- Added filter for rerunning unprocessed bed files based on genome
+
+
 # [0.7.2] - 2025-06-21
 ## Changed:
 - Updated path to the bigbed output folder

requirements/requirements-all.txt

@@ -5,7 +5,7 @@ peppy>=0.40.7
 yacman>=0.8.4
 requests>=2.28.2
 piper>=v0.14.3
-bbconf>=0.11.1
+bbconf>=0.11.3
 # bbconf @ git+https://github.com/databio/bbconf.git@new_bed_compilance#egg=bbconf
 refgenconf>=0.12.2
 pandas>=2.0.0