Merge pull request #92 from sanger-bentley-group/bugfix/srst2-mkfifo-…

…failure Workaround for srst2 mkfifo failure when using latest Nextflow and Singularity
sanger-bentley-group · Sep 18, 2024 · adac009 · adac009
2 parents 8ae19cf + d8e0163
commit adac009
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diff --git a/.gitignore b/.gitignore
@@ -11,3 +11,4 @@ data
 tests/test_data/output/*.txt
 tests/regression_test_data/test_data
 **/__pycache__
+*.img
diff --git a/nextflow.config b/nextflow.config
@@ -89,6 +89,8 @@ profiles {
              enabled = true
              autoMounts = true
              cacheDir = "$PWD"
+            // Prevent mkfifo failure in srst2 with Nextflow 23+ and Singularity
+             runOptions = '-B $(mktemp -d):/tmp'
         }
     }
 }