From 85635678b7e0fbd4b976cb02b8723a9dad137bc1 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Fri, 26 Feb 2021 11:51:30 +0100
Subject: [PATCH 1/3] Make container/conda profiles more strict

---
 .../{{cookiecutter.name_noslash}}/nextflow.config  | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
index d245c91349..e911dc14a9 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
@@ -57,10 +57,18 @@ try {
 }
 
 profiles {
-  conda { process.conda = "$projectDir/environment.yml" }
+  conda { 
+    docker.enabled = false
+    singularity.enabled = false
+    podman.enabled = false
+    process.conda = "$projectDir/environment.yml" 
+    
+    }
   debug { process.beforeScript = 'echo $HOSTNAME' }
   docker {
     docker.enabled = true
+    singularity.enabled = false
+    podman.enabled = false
     // Avoid this error:
     //   WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
     // Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351
@@ -68,10 +76,14 @@ profiles {
     docker.runOptions = '-u \$(id -u):\$(id -g)'
   }
   singularity {
+    docker.enabled = false
     singularity.enabled = true
+    podman.enabled = false
     singularity.autoMounts = true
   }
   podman {
+    singularity.enabled = false
+    docker.enabled = false
     podman.enabled = true
   }
   test { includeConfig 'conf/test.config' }

From 3bc66a543b0bd22d747cbb1a99f3812bf724f7f2 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 26 Feb 2021 12:01:24 +0100
Subject: [PATCH 2/3] Update
 nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config

---
 .../{{cookiecutter.name_noslash}}/nextflow.config              | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
index e911dc14a9..423931d532 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
@@ -62,8 +62,7 @@ profiles {
     singularity.enabled = false
     podman.enabled = false
     process.conda = "$projectDir/environment.yml" 
-    
-    }
+  }
   debug { process.beforeScript = 'echo $HOSTNAME' }
   docker {
     docker.enabled = true

From ec8f8d76aa426b33a678cdf3dcb044117116b05c Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 10 Mar 2021 09:05:38 +0100
Subject: [PATCH 3/3] Added new container configs

---
 .../nextflow.config                           | 21 ++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
index 2cfd62c05e..1659455abf 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
@@ -62,6 +62,8 @@ profiles {
     docker.enabled = false
     singularity.enabled = false
     podman.enabled = false
+    shifter.enabled = false
+    charliecloud = false
     process.conda = "$projectDir/environment.yml" 
   }
   debug { process.beforeScript = 'echo $HOSTNAME' }
@@ -69,6 +71,8 @@ profiles {
     docker.enabled = true
     singularity.enabled = false
     podman.enabled = false
+    shifter.enabled = false
+    charliecloud.enabled = false
     // Avoid this error:
     //   WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
     // Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351
@@ -79,17 +83,32 @@ profiles {
     docker.enabled = false
     singularity.enabled = true
     podman.enabled = false
+    shifter.enabled = false
+    charliecloud.enabled = false
     singularity.autoMounts = true
   }
   podman {
     singularity.enabled = false
     docker.enabled = false
     podman.enabled = true
+    shifter.enabled = false
+    charliecloud = false
   }
   shifter {
+    singularity.enabled = false
+    docker.enabled = false
+    podman.enabled = false
     shifter.enabled = true
+    charliecloud.enabled = false
+  }
+  charliecloud { 
+    includeConfig 'conf/charliecloud.config' 
+    singularity.enabled = false
+    docker.enabled = false
+    podman.enabled = false
+    shifter.enabled = false
+    // charliecloud.enabled is in the dedicated includeConfig
   }
-  charliecloud { includeConfig 'conf/charliecloud.config' }
   test { includeConfig 'conf/test.config' }
   test_full { includeConfig 'conf/test_full.config' }
 }