From 0cd928105f1bc00551e4c23067a682c70be85333 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi <sasha99250@gmail.com>
Date: Tue, 24 Sep 2024 01:15:29 -0400
Subject: [PATCH] fixed few cli bugs and requirements

---
 bedboss/cli.py                    | 8 ++++----
 requirements/requirements-all.txt | 1 +
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/bedboss/cli.py b/bedboss/cli.py
index 76a70b5..4f94f92 100644
--- a/bedboss/cli.py
+++ b/bedboss/cli.py
@@ -148,7 +148,7 @@ def run_pep(
         file_okay=True,
         readable=True,
     ),
-    create_bedset: bool = typer.Option(False, help="Create a new bedset"),
+    create_bedset: bool = typer.Option(True, help="Create a new bedset"),
     bedset_heavy: bool = typer.Option(
         False, help="Run the heavy version of the bedbuncher pipeline"
     ),
@@ -160,9 +160,9 @@ def run_pep(
     force_overwrite: bool = typer.Option(
         False, help="Force overwrite the output files"
     ),
-    upload_qdrant: bool = typer.Option(False, help="Upload to Qdrant"),
-    upload_s3: bool = typer.Option(False, help="Upload to S3"),
-    upload_pephub: bool = typer.Option(False, help="Upload to PEPHub"),
+    upload_qdrant: bool = typer.Option(True, help="Upload to Qdrant"),
+    upload_s3: bool = typer.Option(True, help="Upload to S3"),
+    upload_pephub: bool = typer.Option(True, help="Upload to PEPHub"),
     no_fail: bool = typer.Option(False, help="Do not fail on error"),
     license_id: str = typer.Option(DEFAULT_LICENSE, help="License ID"),
     standardize_pep: bool = typer.Option(False, help="Standardize the PEP using bedMS"),
diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
index 266f16e..51054c7 100644
--- a/requirements/requirements-all.txt
+++ b/requirements/requirements-all.txt
@@ -1,5 +1,6 @@
 logmuse>=0.2.7
 coloredlogs>=15.0.1
+eido>=0.2.3
 peppy>=0.40.6
 yacman>=0.8.4
 requests>=2.28.2