Update all NF-Core modules to latest version which includes no quay.io prefix

modules.json

@@ -7,52 +7,52 @@
                 "nf-core": {
                     "bowtie2/align": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
                         "installed_by": ["modules"]
                     },
                     "bowtie2/build": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "cooler/balance": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "cooler/cload": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "cooler/dump": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "cooler/makebins": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "cooler/zoomify": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "custom/getchromsizes": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     }
                 }

modules/nf-core/bowtie2/align/main.nf

@@ -5,7 +5,7 @@ process BOWTIE2_ALIGN {
     conda "bioconda::bowtie2=2.4.4 bioconda::samtools=1.16.1 conda-forge::pigz=2.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' :
-        'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }"
+        'biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }"
 
     input:
     tuple val(meta) , path(reads)

modules/nf-core/bowtie2/build/main.nf

@@ -5,7 +5,7 @@ process BOWTIE2_BUILD {
     conda "bioconda::bowtie2=2.4.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' :
-        'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }"
+        'biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }"
 
     input:
     tuple val(meta), path(fasta)

modules/nf-core/cooler/balance/main.nf

@@ -5,7 +5,7 @@ process COOLER_BALANCE {
     conda "bioconda::cooler=0.8.11"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0':
-        'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
+        'biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
 
     input:
     tuple val(meta), path(cool), val(resolution)

modules/nf-core/cooler/cload/main.nf

@@ -5,7 +5,7 @@ process COOLER_CLOAD {
     conda "bioconda::cooler=0.8.11"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
-        'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
+        'biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
 
     input:
     tuple val(meta), path(pairs), path(index), val(cool_bin)

modules/nf-core/cooler/dump/main.nf

@@ -5,7 +5,7 @@ process COOLER_DUMP {
     conda "bioconda::cooler=0.8.11"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
-        'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
+        'biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
 
     input:
     tuple val(meta), path(cool), val(resolution)

modules/nf-core/cooler/makebins/main.nf

@@ -5,7 +5,7 @@ process COOLER_MAKEBINS {
     conda "bioconda::cooler=0.8.11"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0':
-        'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
+        'biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
 
     input:
     tuple val(meta), path(chromsizes), val(cool_bin)

modules/nf-core/cooler/zoomify/main.nf

@@ -5,7 +5,7 @@ process COOLER_ZOOMIFY {
     conda "bioconda::cooler=0.8.11"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
-        'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
+        'biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
 
     input:
     tuple val(meta), path(cool)

modules/nf-core/custom/dumpsoftwareversions/main.nf

@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda "bioconda::multiqc=1.13"
+    conda "bioconda::multiqc=1.14"
     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' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
 
     input:
     path versions

modules/nf-core/custom/dumpsoftwareversions/meta.yml

+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: custom_dumpsoftwareversions
 description: Custom module used to dump software versions within the nf-core pipeline template
 keywords:
   - custom
+  - dump
   - version
 tools:
   - custom:

modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py

@@ -3,10 +3,10 @@
 
 """Provide functions to merge multiple versions.yml files."""
 
-import platform
-from textwrap import dedent
 
 import yaml
+import platform
+from textwrap import dedent
 
 
 def _make_versions_html(versions):

modules/nf-core/custom/getchromsizes/main.nf

@@ -5,7 +5,7 @@ process CUSTOM_GETCHROMSIZES {
     conda "bioconda::samtools=1.16.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
-        'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
+        'biocontainers/samtools:1.16.1--h6899075_1' }"
 
     input:
     tuple val(meta), path(fasta)

modules/nf-core/fastqc/main.nf

@@ -5,7 +5,7 @@ process FASTQC {
     conda "bioconda::fastqc=0.11.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
-        'quay.io/biocontainers/fastqc:0.11.9--0' }"
+        'biocontainers/fastqc:0.11.9--0' }"
 
     input:
     tuple val(meta), path(reads)