Merge pull request #2312 from mirpedrol/refgenie-check-path

create .nextflow/nf-core if it doesn't exist
nf-core · Jun 12, 2023 · 1e39535 · 1e39535
2 parents 711d074 + 2c2e2d6
commit 1e39535
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -32,6 +32,7 @@
 
 - GitPod base image: Always self-update to the latest version of Nextflow. Add [pre-commit](https://pre-commit.com/) dependency.
 - GitPod configs: Update Nextflow as an init task, init pre-commit in pipeline config.
+- Refgenie: Create `nxf_home/nf-core/refgenie_genomes.config` path if it doesn't exist ([#2312](https://github.com/nf-core/tools/pull/2312))
 
 # [v2.8 - Ruthenium Monkey](https://github.com/nf-core/tools/releases/tag/2.8) - [2023-04-27]
 

diff --git a/nf_core/refgenie.py b/nf_core/refgenie.py
@@ -184,7 +184,7 @@ def update_config(rgc):
 
     # Save the updated genome config
     try:
-        with open(refgenie_genomes_config_file, "w") as fh:
+        with open(refgenie_genomes_config_file, "w+") as fh:
             fh.write(refgenie_genomes)
         log.info(f"Updated nf-core genomes config: {refgenie_genomes_config_file}")
     except FileNotFoundError: