Attempting to fix testing

sanger-tol · Sep 19, 2023 · 967d21d · 967d21d
1 parent 1956859
commit 967d21d
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Showing 5 changed files with 5 additions and 5 deletions.
diff --git a/modules/local/bamtobed_sort.nf b/modules/local/bamtobed_sort.nf
@@ -4,7 +4,7 @@ process BAMTOBED_SORT {
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-9d3a458f6420e5712103ae2af82c94d26d63f059:60b54b43045e8cf39ba307fd683c69d4c57240ce-0' :
-        'quay.io/biocontainers/mulled-v2-9d3a458f6420e5712103ae2af82c94d26d63f059:60b54b43045e8cf39ba307fd683c69d4c57240ce-0' }"
+        'biocontainers/mulled-v2-9d3a458f6420e5712103ae2af82c94d26d63f059:60b54b43045e8cf39ba307fd683c69d4c57240ce-0' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf b/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf
@@ -4,7 +4,7 @@ process CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT {
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-50d89b457e04ed90fa0cbf8ebc3ae1b9ffbc836b:caf993da1689e8d42f5e4c113ffc9ef81d26df96-0' :
-        'quay.io/biocontainers/mulled-v2-50d89b457e04ed90fa0cbf8ebc3ae1b9ffbc836b:caf993da1689e8d42f5e4c113ffc9ef81d26df96-0' }"
+        'biocontainers/mulled-v2-50d89b457e04ed90fa0cbf8ebc3ae1b9ffbc836b:caf993da1689e8d42f5e4c113ffc9ef81d26df96-0' }"
 
     input:
     tuple val(meta), path(cramfile), path(cramindex), val(from), val(to), val(base), val(chunkid), val(rglines), val(bwaprefix)

diff --git a/modules/local/extract_repeat.nf b/modules/local/extract_repeat.nf
@@ -5,7 +5,7 @@ process EXTRACT_REPEAT {
     conda "conda-forge::perl=5.26.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/perl:5.26.2' :
-        'quay.io/biocontainers/perl:5.26.2' }"
+        'biocontainers/perl:5.26.2' }"
 
     input:
     tuple val( meta ), path( file )

diff --git a/modules/local/findhalfcoverage.nf b/modules/local/findhalfcoverage.nf
@@ -5,7 +5,7 @@ process FINDHALFCOVERAGE {
     conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9' :
-        'quay.io/biocontainers/python:3.9' }"
+        'biocontainers/python:3.9' }"
 
     input:
     tuple val(meta), path(bedfile)

diff --git a/modules/local/graphoverallcoverage.nf b/modules/local/graphoverallcoverage.nf
@@ -5,7 +5,7 @@ process GRAPHOVERALLCOVERAGE {
     conda "conda-forge::perl=5.26.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/perl:5.26.2' :
-        'quay.io/biocontainers/perl:5.26.2' }"
+        'biocontainers/perl:5.26.2' }"
 
     input:
     tuple val(meta), path(bed)