Attempting to fix testing

sanger-tol · Sep 19, 2023 · e2b6777 · e2b6777
1 parent 0ff9bd6
commit e2b6777
Show file tree

Hide file tree

Showing 8 changed files with 8 additions and 8 deletions.
diff --git a/modules/local/extract_telo.nf b/modules/local/extract_telo.nf
@@ -5,7 +5,7 @@ process EXTRACT_TELO {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val( meta ), path( file )

diff --git a/modules/local/find_telomere_windows.nf b/modules/local/find_telomere_windows.nf
@@ -6,7 +6,7 @@ process FIND_TELOMERE_WINDOWS {
     container "${ workflow.containerEngine == 'singularity' &&
                     !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/java-jdk:8.0.112--1' :
-        'quay.io/biocontainers/java-jdk:8.0.112--1' }"
+        'biocontainers/java-jdk:8.0.112--1' }"
 
     input:
     tuple val( meta ), path( file )

diff --git a/modules/local/generate_genome_file.nf b/modules/local/generate_genome_file.nf
@@ -5,7 +5,7 @@ process GENERATE_GENOME_FILE {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val( meta ), path( fai )

diff --git a/modules/local/get_largest_scaff.nf b/modules/local/get_largest_scaff.nf
@@ -6,7 +6,7 @@ process GET_LARGEST_SCAFF {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val( meta ), path( file )

diff --git a/modules/local/getminmaxpunches.nf b/modules/local/getminmaxpunches.nf
@@ -5,7 +5,7 @@ process GETMINMAXPUNCHES{
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(bedfile)

diff --git a/modules/local/reformat_intersect.nf b/modules/local/reformat_intersect.nf
@@ -5,7 +5,7 @@ process REFORMAT_INTERSECT {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val( meta ), path( file )

diff --git a/modules/local/rename_ids.nf b/modules/local/rename_ids.nf
@@ -5,7 +5,7 @@ process RENAME_IDS {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val( meta ), path( file )

diff --git a/modules/local/replace_dots.nf b/modules/local/replace_dots.nf
@@ -5,7 +5,7 @@ process REPLACE_DOTS {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val( meta ), path( file )