From 77dc34864162f43989050edcbb1bb25f25e7baf7 Mon Sep 17 00:00:00 2001
From: Harry Hung <4848896+HarryHung@users.noreply.github.com>
Date: Tue, 17 Sep 2024 23:58:30 +0000
Subject: [PATCH 1/2] Add workaround for mkfifo failure in srst2 with Nextflow
 23+ and Singularity

---
 nextflow.config | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nextflow.config b/nextflow.config
index 5f186b9..73c402b 100644
--- 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'
         }
     }
 }

From d8e01631430f0c8ba5355ecc9cc8c5af23641748 Mon Sep 17 00:00:00 2001
From: Harry Hung <4848896+HarryHung@users.noreply.github.com>
Date: Wed, 18 Sep 2024 10:21:33 +0100
Subject: [PATCH 2/2] Ignore Singularity image

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index deec0ac..de5fc34 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,3 +11,4 @@ data
 tests/test_data/output/*.txt
 tests/regression_test_data/test_data
 **/__pycache__
+*.img