diff --git a/modules/local/cooltools/eigscis.nf b/modules/local/cooltools/eigscis.nf
index feaa30007099cae34a18eaa8105a3367e260e1b6..873bd243cd02102f327cba853197d39bc0ea860e 100644
--- a/modules/local/cooltools/eigscis.nf
+++ b/modules/local/cooltools/eigscis.nf
@@ -9,7 +9,7 @@ process COOLTOOLS_EIGSCIS {
     conda "bioconda::cooltools=0.5.1 bioconda::ucsc-bedgraphtobigwig=377"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' :
-        'quay.io/biocontainers/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' }"
+        'biocontainers/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' }"
 
     input:
     tuple val(meta), path(cool), val(resolution)
diff --git a/modules/local/cooltools/insulation.nf b/modules/local/cooltools/insulation.nf
index 8a9127ea47824f9541c4faf2263d8e61030468c3..af53529ef80baa12dbd81bd0a2b8fa3ec2122cfa 100644
--- a/modules/local/cooltools/insulation.nf
+++ b/modules/local/cooltools/insulation.nf
@@ -9,7 +9,7 @@ process COOLTOOLS_INSULATION {
     conda "bioconda::cooltools=0.5.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/cooltools:0.5.1--py37h37892f8_0' :
-        'quay.io/biocontainers/cooltools:0.5.1--py37h37892f8_0' }"
+        'biocontainers/cooltools:0.5.1--py37h37892f8_0' }"
 
     input:
     tuple val(meta), path(cool)
diff --git a/modules/local/hicexplorer/hicFindTADs.nf b/modules/local/hicexplorer/hicFindTADs.nf
index b6cae335c22111407b3d782e95a067ed087645e0..d86dc837e29e56aa4ba88cd2c66962444046647b 100644
--- a/modules/local/hicexplorer/hicFindTADs.nf
+++ b/modules/local/hicexplorer/hicFindTADs.nf
@@ -8,7 +8,7 @@ process HIC_FIND_TADS {
     conda "bioconda::hicexplorer=3.7.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
-        'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
+        'biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
 
     input:
     tuple val(meta), path(cool)
diff --git a/modules/local/hicexplorer/hicPlotDistVsCounts.nf b/modules/local/hicexplorer/hicPlotDistVsCounts.nf
index 3e37d3fe7b466dbe45b2f19c220e2f9a65a07a9a..1143a05d3767ba4a9289e6f423cb7dc768d3d197 100644
--- a/modules/local/hicexplorer/hicPlotDistVsCounts.nf
+++ b/modules/local/hicexplorer/hicPlotDistVsCounts.nf
@@ -9,7 +9,7 @@ process HIC_PLOT_DIST_VS_COUNTS {
     conda "bioconda::hicexplorer=3.7.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
-        'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
+        'biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
 
     input:
     tuple val(meta), path(cool)
diff --git a/modules/local/hicpro/bowtie2_merge.nf b/modules/local/hicpro/bowtie2_merge.nf
index 7a4e96be9aaf2470a10ca19672591e0f84853602..64aa6e6c05fd9e729ac26a0704f33b802f7dbb0c 100644
--- a/modules/local/hicpro/bowtie2_merge.nf
+++ b/modules/local/hicpro/bowtie2_merge.nf
@@ -5,7 +5,7 @@ process MERGE_BOWTIE2{
     conda "bioconda::samtools=1.15.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+        'biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
     tuple val(meta), path(bam1), path(bam2)
diff --git a/modules/local/hicpro/build_contact_maps.nf b/modules/local/hicpro/build_contact_maps.nf
index fd633a984f26b4cccc901a92e983cf0acfaa8eed..8ff454039ffd0de513160fe0ecec4e7519d4fe42 100644
--- a/modules/local/hicpro/build_contact_maps.nf
+++ b/modules/local/hicpro/build_contact_maps.nf
@@ -5,15 +5,15 @@ process BUILD_CONTACT_MAPS{
   conda "conda-forge::sed=4.7"
   container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
       'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-      'ubuntu:20.04' }"
+      'quay.io/nfcore/ubuntu:20.04' }"
 
   input:
-  tuple val(meta), path(vpairs), val(resolution) 
-  tuple val(meta2), path(chrsize) 
+  tuple val(meta), path(vpairs), val(resolution)
+  tuple val(meta2), path(chrsize)
 
   output:
   tuple val(meta), val(resolution), path("*.matrix"), path("*.bed"), emit: maps
-   
+
   script:
   def prefix = task.ext.prefix ?: "${meta.id}"
   """
diff --git a/modules/local/hicpro/combine_mates.nf b/modules/local/hicpro/combine_mates.nf
index da95be819a03560d75db2bc80ab3e8b72bf774aa..b0d828e3200bcb00fb4b94dcb071091ae352b7f7 100644
--- a/modules/local/hicpro/combine_mates.nf
+++ b/modules/local/hicpro/combine_mates.nf
@@ -5,7 +5,7 @@ process COMBINE_MATES {
     conda "conda-forge::python=3.9  bioconda::pysam=0.19.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
-        'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+        'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/local/hicpro/dnase_mapping_stats.nf b/modules/local/hicpro/dnase_mapping_stats.nf
index 64cb0792e4d93dfcc1b1e7d0b5d50bf7e0b75c73..8e85113944f79dc0b155ee9be441b2badf5c0245 100644
--- a/modules/local/hicpro/dnase_mapping_stats.nf
+++ b/modules/local/hicpro/dnase_mapping_stats.nf
@@ -5,7 +5,7 @@ process MAPPING_STATS_DNASE {
     conda "bioconda::samtools=1.15.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+        'biocontainers/samtools:1.15.1--h1170115_0' }"
 
 
     input:
diff --git a/modules/local/hicpro/get_restriction_fragments.nf b/modules/local/hicpro/get_restriction_fragments.nf
index affc2d986a339d239602c6e66ad6f0d50517505e..56cd74a24a7d5102aad25cbe7032e31e2c4a1452 100644
--- a/modules/local/hicpro/get_restriction_fragments.nf
+++ b/modules/local/hicpro/get_restriction_fragments.nf
@@ -5,7 +5,7 @@ process GET_RESTRICTION_FRAGMENTS {
     conda "conda-forge::python=3.9 conda-forge::numpy=1.22.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
-        'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+        'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/local/hicpro/get_valid_interaction.nf b/modules/local/hicpro/get_valid_interaction.nf
index cc148371e52e04e96ca8dc9461a46ce80216b85e..bebd42197471c214ce0cde63c88ea89224387e76 100644
--- a/modules/local/hicpro/get_valid_interaction.nf
+++ b/modules/local/hicpro/get_valid_interaction.nf
@@ -5,7 +5,7 @@ process GET_VALID_INTERACTION {
     conda "conda-forge::python=3.9  bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
-        'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+        'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/local/hicpro/get_valid_interaction_dnase.nf b/modules/local/hicpro/get_valid_interaction_dnase.nf
index 142d0cbd4f042fb0106c7e0380515f7b54c79953..d62318f87feac914b8b07796792fa18e363eef7e 100644
--- a/modules/local/hicpro/get_valid_interaction_dnase.nf
+++ b/modules/local/hicpro/get_valid_interaction_dnase.nf
@@ -5,7 +5,7 @@ process GET_VALID_INTERACTION_DNASE {
     conda "conda-forge::python=3.9 bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
-        'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+        'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/local/hicpro/hicpro2pairs.nf b/modules/local/hicpro/hicpro2pairs.nf
index 2ba2a901b62791e733900b24da4f244cd2fbaba7..eb9b86b5e4ca0ace6549fe0c33a9dd1f63aaf5f3 100644
--- a/modules/local/hicpro/hicpro2pairs.nf
+++ b/modules/local/hicpro/hicpro2pairs.nf
@@ -5,7 +5,7 @@ process HICPRO2PAIRS {
     conda "bioconda::pairix=0.3.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' :
-        'quay.io/biocontainers/pairix:0.3.7--py36h30a8e3e_3' }"
+        'biocontainers/pairix:0.3.7--py36h30a8e3e_3' }"
 
     input:
     tuple val(meta), path(vpairs)
diff --git a/modules/local/hicpro/merge_stats.nf b/modules/local/hicpro/merge_stats.nf
index b25dc8a13d2f18bc5ae05742c5f15d77fd19627d..d9c2aecb5b2eb5c7574e139f7ffbbf3c8d3289de 100644
--- a/modules/local/hicpro/merge_stats.nf
+++ b/modules/local/hicpro/merge_stats.nf
@@ -5,7 +5,7 @@ process MERGE_STATS {
     conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
-        'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+        'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
 
     input:
     tuple val(meta), path(fstat)
diff --git a/modules/local/hicpro/merge_valid_interaction.nf b/modules/local/hicpro/merge_valid_interaction.nf
index 29e568a20997c0a313a87cf964f1f8c10327228b..6a5c830bb58dfadeab551af1c46aef433bbfeff1 100644
--- a/modules/local/hicpro/merge_valid_interaction.nf
+++ b/modules/local/hicpro/merge_valid_interaction.nf
@@ -5,7 +5,7 @@ process MERGE_VALID_INTERACTION {
     conda "conda-forge::gawk=5.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'nfcore/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(vpairs)
diff --git a/modules/local/hicpro/run_ice.nf b/modules/local/hicpro/run_ice.nf
index 0a435edcd0f2a82c93be2a1b9bd832a721c270cf..74c96dc828399461d725fc52752cf98337b5dc02 100644
--- a/modules/local/hicpro/run_ice.nf
+++ b/modules/local/hicpro/run_ice.nf
@@ -5,7 +5,7 @@ process ICE_NORMALIZATION{
     conda "conda-forge::python=3.9 bioconda::iced=0.5.10 conda-forge::numpy=1.22.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
-        'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
+        'biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
 
     input:
     tuple val(meta), val(res), path(rmaps), path(bed)
diff --git a/modules/local/hicpro/trim_reads.nf b/modules/local/hicpro/trim_reads.nf
index 5a96df412ea89845583fc363eccf2df49ba9458d..f6d2e90cdd1f82c13a5ee54b87d8b0456e42469f 100644
--- a/modules/local/hicpro/trim_reads.nf
+++ b/modules/local/hicpro/trim_reads.nf
@@ -5,7 +5,7 @@ process TRIM_READS {
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'nfcore/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
index 595dc94d0eebd849d217c25349e4bb253bee64b6..6f6bad458bb8d83962f1d5a1bc922caeb7d3d9f9 100644
--- a/modules/local/multiqc.nf
+++ b/modules/local/multiqc.nf
@@ -4,7 +4,7 @@ process MULTIQC {
     conda "bioconda::multiqc=1.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
+        'biocontainers/multiqc:1.13--pyhdfd78af_0' }"
 
     input:
     path multiqc_config
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
index 1624dfafe6425f07bbd15daf3b2735ea1187c0ec..096c80b0bd37b9a40bbf61cdefa13007f58b0c5d 100644
--- a/modules/local/samplesheet_check.nf
+++ b/modules/local/samplesheet_check.nf
@@ -5,7 +5,7 @@ process SAMPLESHEET_CHECK {
     conda "conda-forge::python=3.8.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.8.3' :
-        'quay.io/biocontainers/python:3.8.3' }"
+        'biocontainers/python:3.8.3' }"
 
     input:
     path samplesheet
diff --git a/modules/local/split_cooler_dump.nf b/modules/local/split_cooler_dump.nf
index 8b9e45b31d304545ea62946f4c4e0eacb7860002..c9dde0086009d46c9d04a5342f3197a9d211653e 100644
--- a/modules/local/split_cooler_dump.nf
+++ b/modules/local/split_cooler_dump.nf
@@ -5,7 +5,7 @@ process SPLIT_COOLER_DUMP {
     conda "conda-forge::gawk=5.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'nfcore/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(bedpe)