From a632db8be055f7b0dc05b0f366be5bd71c8cb21e Mon Sep 17 00:00:00 2001
From: rernst <r.f.ernst-3@umcutrecht.nl>
Date: Fri, 16 Dec 2022 10:54:16 +0100
Subject: [PATCH 1/2] Add sylabs uri

---
 BWA-Mapping/bwa-0.7.17_samtools-1.9/Mapping.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BWA-Mapping/bwa-0.7.17_samtools-1.9/Mapping.nf b/BWA-Mapping/bwa-0.7.17_samtools-1.9/Mapping.nf
index 9eea8727..c85804ee 100644
--- a/BWA-Mapping/bwa-0.7.17_samtools-1.9/Mapping.nf
+++ b/BWA-Mapping/bwa-0.7.17_samtools-1.9/Mapping.nf
@@ -2,7 +2,7 @@ process BWAMapping {
     tag {"BWA Mem ${sample_id} - ${rg_id}"}
     label 'BWA_0_7_17'
     label 'BWA_0_7_17_Mem'
-    container = 'library://sawibo/default/bioinf-tools:bwa-0.7.17_samtools-1.9'
+    container = 'library://library.sylabs.io/sawibo/default/bioinf-tools:bwa-0.7.17_samtools-1.9'
     shell = ['/bin/bash', '-euo', 'pipefail']
     
     input:

From ee9605d01b9a21b2cb3fba002fdf064f6ef39c81 Mon Sep 17 00:00:00 2001
From: rernst <r.f.ernst-3@umcutrecht.nl>
Date: Fri, 16 Dec 2022 14:17:27 +0100
Subject: [PATCH 2/2] Add sylabs uri

---
 ControlFREEC/11.5/AssessSignificance.nf | 2 +-
 ControlFREEC/11.5/Freec.nf              | 3 +--
 ControlFREEC/11.5/MakeGraph.nf          | 2 +-
 ControlFREEC/11.5/MakeKaryotype.nf      | 2 +-
 4 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/ControlFREEC/11.5/AssessSignificance.nf b/ControlFREEC/11.5/AssessSignificance.nf
index d4ce7af5..cd5d46ec 100644
--- a/ControlFREEC/11.5/AssessSignificance.nf
+++ b/ControlFREEC/11.5/AssessSignificance.nf
@@ -2,7 +2,7 @@ process AssessSignificance {
     tag {"Control Freec AssessSignificance ${sample_id}"}
     label 'ControlFreec_11_5'
     label 'ControlFreec_11_5_AssessSignificance'
-    container = 'library://sawibo/default/bioinf-tools:freec11.5'
+    container = 'library://library.sylabs.io/sawibo/default/bioinf-tools:freec11.5'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
diff --git a/ControlFREEC/11.5/Freec.nf b/ControlFREEC/11.5/Freec.nf
index c9422fcc..d6ed6595 100644
--- a/ControlFREEC/11.5/Freec.nf
+++ b/ControlFREEC/11.5/Freec.nf
@@ -2,8 +2,7 @@ process Freec {
     tag {"Control Freec ${sample_id}"}
     label 'ControlFreec_11_5'
     label 'ControlFreec_11_5_Freec'
-    //TODO: upload to singularity library
-    container = 'library://sawibo/default/bioinf-tools:freec11.5'
+    container = 'library://library.sylabs.io/sawibo/default/bioinf-tools:freec11.5'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
diff --git a/ControlFREEC/11.5/MakeGraph.nf b/ControlFREEC/11.5/MakeGraph.nf
index 3375d31b..fb53cafb 100644
--- a/ControlFREEC/11.5/MakeGraph.nf
+++ b/ControlFREEC/11.5/MakeGraph.nf
@@ -2,7 +2,7 @@ process MakeGraph {
     tag {"Control Freec MakeGraph ${sample_id}"}
     label 'ControlFreec_11_5'
     label 'ControlFreec_11_5_MakeGraph'
-    container = 'library://sawibo/default/bioinf-tools:freec11.5'
+    container = 'library://library.sylabs.io/sawibo/default/bioinf-tools:freec11.5'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
diff --git a/ControlFREEC/11.5/MakeKaryotype.nf b/ControlFREEC/11.5/MakeKaryotype.nf
index a903e8d2..312b3f96 100644
--- a/ControlFREEC/11.5/MakeKaryotype.nf
+++ b/ControlFREEC/11.5/MakeKaryotype.nf
@@ -2,7 +2,7 @@ process MakeKaryotype {
     tag {"Control Freec MakeKaryotype ${sample_id}"}
     label 'ControlFreec_11_5'
     label 'ControlFreec_11_5_MakeKaryotype'
-    container = 'library://sawibo/default/bioinf-tools:freec11.5'
+    container = 'library://library.sylabs.io/sawibo/default/bioinf-tools:freec11.5'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input: