Merge pull request #396 from nf-core/patch

Prevent bioawk overwriting input files if input and module output names the same
nf-core · Jul 8, 2024 · 2a5c32a · 2a5c32a
2 parents ec1f1b6 + d968423
commit 2a5c32a
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,16 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.1.6 - [2024-07-08]
+
+### `Added`
+
+### `Fixed`
+
+- [#396](https://github.com/nf-core/funcscan/pull/396) Fixed bioawk overwriting input files. (❤️ to @Microbion for reporting, fix by @jfy133)
+
+### `Dependencies`
+
 ## v1.1.5 - [2024-03-20]
 
 ### `Added`

diff --git a/modules.json b/modules.json
@@ -57,7 +57,7 @@
                     },
                     "bioawk": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "dee3479f3b4a828df6052d318403d2b6a87b2d2e",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/bioawk/bioawk.diff"
                     },
@@ -88,7 +88,7 @@
                     },
                     "fargene": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "a7231cbccb86535529e33859e05d19ac93f3ea04",
                         "installed_by": ["modules"]
                     },
                     "gecco/run": {

diff --git a/modules/nf-core/bioawk/environment.yml b/modules/nf-core/bioawk/environment.yml
diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf
diff --git a/modules/nf-core/bioawk/meta.yml b/modules/nf-core/bioawk/meta.yml
diff --git a/modules/nf-core/fargene/environment.yml b/modules/nf-core/fargene/environment.yml
diff --git a/modules/nf-core/fargene/main.nf b/modules/nf-core/fargene/main.nf
diff --git a/modules/nf-core/fargene/meta.yml b/modules/nf-core/fargene/meta.yml
diff --git a/nextflow.config b/nextflow.config
@@ -269,6 +269,7 @@ profiles {
         shifter.enabled        = false
         charliecloud.enabled   = false
         apptainer.enabled      = false
+        docker.runOptions       = '-u $(id -u):$(id -g)'
     }
     arm {
         docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'