Update local modules

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)

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)

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)

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)

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)

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}"
   """

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)

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:

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)

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)

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)

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)

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)

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)

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)

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)

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

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

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)