From 848ba9fd840700b8e6b079f4a04d63ac89ade4fe Mon Sep 17 00:00:00 2001
From: Ronak Shah <shahr2@mskcc.org>
Date: Fri, 6 Sep 2024 10:45:23 -0400
Subject: [PATCH] Updating submodules and fixing git action

---
 .travis.yml        |  4 ++--
 command_line_tools |  2 +-
 requirements.txt   | 22 ++++++----------------
 setup.cfg          |  2 +-
 setup.py           |  2 +-
 subworkflows       |  2 +-
 tox.ini            |  6 +++---
 7 files changed, 15 insertions(+), 25 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 35ba11b..ff94130 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,6 +1,6 @@
 language: python
 python:
-- 3.6
+- 3.10
 install: pip install -U tox-travis
 script: tox
 deploy:
@@ -14,4 +14,4 @@ deploy:
   on:
     tags: true
     repo: msk-access/bam_collapsing
-    python: 3.6
+    python: 3.10
diff --git a/command_line_tools b/command_line_tools
index 5aae434..082f3a3 160000
--- a/command_line_tools
+++ b/command_line_tools
@@ -1 +1 @@
-Subproject commit 5aae4345e0b2ac631ee2584042dc7c433431398c
+Subproject commit 082f3a3177a845acfd717ad1783ae5b6a668095e
diff --git a/requirements.txt b/requirements.txt
index 6217b4e..b9ba408 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,16 +1,6 @@
-toil[cwl]==5.0.0
-pytz==2020.1
-typing==3.7.4.3
-ruamel.yaml==0.16.5
-pip==20.2.3
-bumpversion==0.6.0
-wheel==0.35.1
-watchdog==0.10.3
-flake8==3.8.4
-tox==3.20.0
-coverage==5.3
-twine==3.2.0
-pytest==6.1.1
-pytest-runner==5.2
-coloredlogs==10.0
-pytest-travis-fold==1.3.0
+coloredlogs==15.0.1
+pytest==7.2.0
+setuptools==65.4.1
+toil[cwl]==5.10.0
+pytest-runner==6.0.0
+tox==3.27.1
diff --git a/setup.cfg b/setup.cfg
index a64e852..108252d 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.0
+current_version = 1.1.0
 commit = True
 tag = True
 
diff --git a/setup.py b/setup.py
index 09f2dbb..4bad80b 100644
--- a/setup.py
+++ b/setup.py
@@ -8,7 +8,7 @@
 with open('README.md') as readme_file:
     readme = readme_file.read()
 
-requirements = ['toil[all]==4.2.0', ]
+requirements = ['toil[all]==5.10.0', ]
 
 setup_requirements = [
     'pytest-runner', ]
diff --git a/subworkflows b/subworkflows
index e6aa311..aeb7fec 160000
--- a/subworkflows
+++ b/subworkflows
@@ -1 +1 @@
-Subproject commit e6aa31182783696debaa222c100087f3d9210ac0
+Subproject commit aeb7fec838db8abdfbdae7fbc617e2dd6bc5ae9c
diff --git a/tox.ini b/tox.ini
index 0e1a5dd..3889ce9 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,13 +1,13 @@
 [tox]
-envlist = py{36}-{linux}
+envlist = py{310}-{linux}
 
 [travis]
 python =
-    3.6: py36
+    3.10: py310
 
 [gh-actions]
 python =
-    3.6: py36
+    3.10: py310
 
 [gh-actions:env]
 PLATFORM =