Resolve intervals path (#160)

* Resolve intervals before split * Bump version to 10.0.1
uclahs-cds · Apr 16, 2024 · d93a6e2 · d93a6e2
1 parent f42b9ae
commit d93a6e2
Show file tree

Hide file tree

Showing 3 changed files with 8 additions and 2 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,9 +8,15 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
+
+---
+
+## [10.0.1] - 2024-04-15
 ### Changed
 - Replace workflow diagram with PlantUML version
 - Update PlantUML action to v1.0.1
+### Fixed
+- Resolve intervals before splitting to allow for index discovery
 
 ---
 

diff --git a/module/split-intervals.nf b/module/split-intervals.nf
@@ -42,7 +42,7 @@ process run_SplitIntervals_GATK {
     set -euo pipefail
     gatk SplitIntervals \
         -R ${reference} \
-        -L ${intervals} \
+        -L "\$(realpath ${intervals})" \
         --scatter-count ${params.scatter_count} \
         ${subdivision_mode} \
         ${params.split_intervals_extra_args} \

diff --git a/nextflow.config b/nextflow.config
@@ -5,5 +5,5 @@ manifest {
     name = 'call-gSNP'
     author = ["Yash Patel", "Shu Tao", "Stefan Eng"]
     description = 'Nextflow pipeline to call germline short variants in single or normal-tumour paired mode'
-    version = '10.0.0'
+    version = '10.0.1'
 }