From 19fe13b5c8103bb5cd91e97df7525694f2c88ebe Mon Sep 17 00:00:00 2001
From: Yash Patel <86321070+yashpatel6@users.noreply.github.com>
Date: Wed, 15 May 2024 17:10:27 -0700
Subject: [PATCH] Release `v10.1.0` (#314)

* Bump version for release

* Autofix Nextflow configuration regression tests

---------

Co-authored-by: yashpatel6 <yashpatel6@users.noreply.github.com>
---
 CHANGELOG.md             |  2 ++
 nextflow.config          |  2 +-
 test/configtest-F16.json | 12 ++++++------
 3 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a383646..e0d12ad 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+
+## [10.1.0] - 2024-05-15
 ### Changed
 - Update Picard version to 3.1.1
 - Update BWA-MEM2, HISAT2 images to use SAMTools version 1.17
diff --git a/nextflow.config b/nextflow.config
index 6ed40c5..c6205ee 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -2,5 +2,5 @@ manifest {
     name = "align-DNA"
     author = "Benjamin Carlin; Chenghao Zhu; Aaron Holmes; Yash Patel; Nicole Zeltser; Jieun Oh; Jaron Arbet"
     description = "alignment pipeline for paired fastqs DNA samples"
-    version = "10.0.0"
+    version = "10.1.0"
     }
diff --git a/test/configtest-F16.json b/test/configtest-F16.json
index d99d4c4..6b0a08d 100644
--- a/test/configtest-F16.json
+++ b/test/configtest-F16.json
@@ -34,7 +34,7 @@
       "author": "Benjamin Carlin; Chenghao Zhu; Aaron Holmes; Yash Patel; Nicole Zeltser; Jieun Oh; Jaron Arbet",
       "description": "alignment pipeline for paired fastqs DNA samples",
       "name": "align-DNA",
-      "version": "10.0.0"
+      "version": "10.1.0"
     },
     "params": {
       "aligner": [
@@ -73,7 +73,7 @@
           }
         ]
       },
-      "log_output_dir": "/tmp/outputs/align-DNA-10.0.0/a_mini_n2_picard/log-align-DNA-10.0.0-19970704T165655Z/",
+      "log_output_dir": "/tmp/outputs/align-DNA-10.1.0/a_mini_n2_picard/log-align-DNA-10.1.0-19970704T165655Z/",
       "make_duplicates": true,
       "mark_duplicates": true,
       "max_cpus": "16",
@@ -81,7 +81,7 @@
       "min_cpus": "1",
       "min_memory": "1 MB",
       "output_dir": "/tmp/outputs",
-      "output_dir_base": "/tmp/outputs/align-DNA-10.0.0/a_mini_n2_picard",
+      "output_dir_base": "/tmp/outputs/align-DNA-10.1.0/a_mini_n2_picard",
       "picardtools_version": "3.1.1",
       "pipeval_version": "4.0.0-rc.2",
       "proc_resource_params": {
@@ -285,15 +285,15 @@
     },
     "report": {
       "enabled": true,
-      "file": "/tmp/outputs/align-DNA-10.0.0/a_mini_n2_picard/log-align-DNA-10.0.0-19970704T165655Z//nextflow-log/report.html"
+      "file": "/tmp/outputs/align-DNA-10.1.0/a_mini_n2_picard/log-align-DNA-10.1.0-19970704T165655Z//nextflow-log/report.html"
     },
     "timeline": {
       "enabled": true,
-      "file": "/tmp/outputs/align-DNA-10.0.0/a_mini_n2_picard/log-align-DNA-10.0.0-19970704T165655Z//nextflow-log/timeline.html"
+      "file": "/tmp/outputs/align-DNA-10.1.0/a_mini_n2_picard/log-align-DNA-10.1.0-19970704T165655Z//nextflow-log/timeline.html"
     },
     "trace": {
       "enabled": true,
-      "file": "/tmp/outputs/align-DNA-10.0.0/a_mini_n2_picard/log-align-DNA-10.0.0-19970704T165655Z//nextflow-log/trace.txt"
+      "file": "/tmp/outputs/align-DNA-10.1.0/a_mini_n2_picard/log-align-DNA-10.1.0-19970704T165655Z//nextflow-log/trace.txt"
     },
     "workDir": "/scratch/8543"
   }