refactor: Support container_registry in modules

modules/nf-core/abacas/main.nf

@@ -3,9 +3,8 @@ process ABACAS {
     label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::abacas=1.3.1" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/abacas:1.3.1--pl526_0' :
-        'quay.io/biocontainers/abacas:1.3.1--pl526_0' }"
+    def container_image = "abacas:1.3.1--pl526_0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(scaffold)

modules/nf-core/abricate/run/main.nf

@@ -3,9 +3,8 @@ process ABRICATE_RUN {
     label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
-        'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
+    def container_image = "abricate:1.0.1--ha8f3691_1"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(assembly)

modules/nf-core/abricate/summary/main.nf

@@ -3,9 +3,8 @@ process ABRICATE_SUMMARY {
     label 'process_single'
 
     conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
-        'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
+    def container_image = "abricate:1.0.1--ha8f3691_1"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(reports)

modules/nf-core/adapterremoval/main.nf

@@ -3,9 +3,8 @@ process ADAPTERREMOVAL {
     label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' :
-        'quay.io/biocontainers/adapterremoval:2.3.2--hb7ba0dd_0' }"
+    def container_image = "adapterremoval:2.3.2--hb7ba0dd_0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(reads)

modules/nf-core/adapterremovalfixprefix/main.nf

@@ -4,9 +4,8 @@ process ADAPTERREMOVALFIXPREFIX {
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2':
-        'quay.io/biocontainers/adapterremovalfixprefix:0.0.5--hdfd78af_2' }"
+    def container_image = "adapterremovalfixprefix:0.0.5--hdfd78af_2"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(fastq)

modules/nf-core/agrvate/main.nf

@@ -3,9 +3,8 @@ process AGRVATE {
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::agrvate=1.0.2" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/agrvate:1.0.2--hdfd78af_0' :
-        'quay.io/biocontainers/agrvate:1.0.2--hdfd78af_0' }"
+    def container_image = "agrvate:1.0.2--hdfd78af_0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(fasta)

modules/nf-core/allelecounter/main.nf

@@ -3,9 +3,8 @@ process ALLELECOUNTER {
     label 'process_low'
 
     conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0' :
-        'quay.io/biocontainers/cancerit-allelecount:4.3.0--h41abebc_0' }"
+    def container_image = "cancerit-allelecount:4.3.0--h41abebc_0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(input), path(input_index)

modules/nf-core/ampir/main.nf

@@ -3,9 +3,8 @@ process AMPIR {
     label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::r-ampir=1.1.0" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-ampir:1.1.0':
-        'quay.io/biocontainers/r-ampir:1.1.0' }"
+    def container_image = "r-ampir:1.1.0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(faa)

modules/nf-core/amplify/predict/main.nf

@@ -4,9 +4,8 @@ process AMPLIFY_PREDICT {
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::amplify=1.0.3" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/amplify:1.0.3--py36hdfd78af_0':
-        'quay.io/biocontainers/amplify:1.0.3--py36hdfd78af_0' }"
+    def container_image = "amplify:1.0.3--py36hdfd78af_0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(faa)

modules/nf-core/amps/main.nf

@@ -2,9 +2,8 @@ process AMPS {
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::hops=0.35" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' :
-        'quay.io/biocontainers/hops:0.35--hdfd78af_1' }"
+    def container_image = "hops:0.35--hdfd78af_1"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     path maltextract_results

modules/nf-core/amrfinderplus/run/main.nf

@@ -3,9 +3,8 @@ process AMRFINDERPLUS_RUN {
     label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0':
-        'quay.io/biocontainers/ncbi-amrfinderplus:3.10.30--h6e70893_0' }"
+    def container_image = "ncbi-amrfinderplus:3.10.30--h6e70893_0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(fasta)

modules/nf-core/amrfinderplus/update/main.nf

@@ -3,9 +3,8 @@ process AMRFINDERPLUS_UPDATE {
     label 'process_single'
 
     conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0':
-        'quay.io/biocontainers/ncbi-amrfinderplus:3.10.30--h6e70893_0' }"
+    def container_image = "ncbi-amrfinderplus:3.10.30--h6e70893_0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     output:
     path "amrfinderdb.tar.gz", emit: db

modules/nf-core/angsd/docounts/main.nf

@@ -3,9 +3,8 @@ process ANGSD_DOCOUNTS {
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::angsd=0.939" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/angsd:0.939--h468462d_0':
-        'quay.io/biocontainers/angsd:0.939--h468462d_0' }"
+    def container_image = "angsd:0.939--h468462d_0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(bam), path(bai), path(minqfile)

modules/nf-core/antismash/antismashlite/main.nf

@@ -3,9 +3,8 @@ process ANTISMASH_ANTISMASHLITE {
     label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' :
-        'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
+    def container_image = "antismash-lite:6.0.1--pyhdfd78af_1"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     containerOptions {
         workflow.containerEngine == 'singularity' ?

modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf

@@ -2,9 +2,8 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
     label 'process_single'
 
     conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' :
-        'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
+    def container_image = "antismash-lite:6.0.1--pyhdfd78af_1"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     /*
     These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH.
@@ -14,9 +13,9 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
 
     containerOptions {
         workflow.containerEngine == 'singularity' ?
-        "-B $database_css:/usr/local/lib/python3.8/site-packages/antismash/outputs/html/css,$database_detection:/usr/local/lib/python3.8/site-packages/antismash/detection,$database_modules:/usr/local/lib/python3.8/site-packages/antismash/modules" :
+        "-B $antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
         workflow.containerEngine == 'docker' ?
-        "-v \$PWD/$database_css:/usr/local/lib/python3.8/site-packages/antismash/outputs/html/css -v \$PWD/$database_detection:/usr/local/lib/python3.8/site-packages/antismash/detection -v \$PWD/$database_modules:/usr/local/lib/python3.8/site-packages/antismash/modules" :
+        "-v \$PWD/$antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
         ''
         }
 

modules/nf-core/aria2/main.nf

@@ -4,9 +4,8 @@ process ARIA2 {
     label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::aria2=1.36.0" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/aria2:1.36.0' :
-        'quay.io/biocontainers/aria2:1.36.0' }"
+    def container_image = "aria2:1.36.0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     val source_url

modules/nf-core/ariba/getref/main.nf

@@ -3,9 +3,8 @@ process ARIBA_GETREF {
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3':
-        'quay.io/biocontainers/ariba:2.14.6--py39h67e14b5_3' }"
+    def container_image = "ariba:2.14.6--py39h67e14b5_3"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     val(db_name)

modules/nf-core/ariba/run/main.nf

@@ -3,9 +3,8 @@ process ARIBA_RUN {
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3':
-        'quay.io/biocontainers/ariba:2.14.6--py39h67e14b5_3' }"
+    def container_image = "ariba:2.14.6--py39h67e14b5_3"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(reads)

modules/nf-core/arriba/main.nf

@@ -3,9 +3,8 @@ process ARRIBA {
     label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::arriba=2.3.0" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/arriba:2.3.0--haa8aa89_0' :
-        'quay.io/biocontainers/arriba:2.3.0--haa8aa89_0' }"
+    def container_image = "arriba:2.3.0--haa8aa89_0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(bam)

modules/nf-core/artic/guppyplex/main.nf

@@ -3,9 +3,8 @@ process ARTIC_GUPPYPLEX {
     label 'process_high'
 
     conda (params.enable_conda ? "bioconda::artic=1.2.2" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/artic:1.2.2--pyhdfd78af_0' :
-        'quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0' }"
+    def container_image = "artic:1.2.2--pyhdfd78af_0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(fastq_dir)

modules/nf-core/artic/minion/main.nf

@@ -3,9 +3,8 @@ process ARTIC_MINION {
     label 'process_high'
 
     conda (params.enable_conda ? "bioconda::artic=1.2.2" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/artic:1.2.2--pyhdfd78af_0' :
-        'quay.io/biocontainers/artic:1.2.2--pyhdfd78af_0' }"
+    def container_image = "artic:1.2.2--pyhdfd78af_0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(fastq)

modules/nf-core/ascat/main.nf

@@ -3,9 +3,8 @@ process ASCAT {
     label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount=4.3.0" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0':
-        'quay.io/biocontainers/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0' }"
+    def container_image = "mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor)
@@ -84,7 +83,6 @@ process ASCAT {
         $skip_allele_counting_normal_arg
     )
 
-
     #Load the data
     ascat.bc = ascat.loadData(
         Tumor_LogR_file = paste0("$prefix", ".tumour_tumourLogR.txt"),
@@ -195,5 +193,4 @@ process ASCAT {
 
     """
 
-
 }

modules/nf-core/assemblyscan/main.nf

@@ -3,9 +3,8 @@ process ASSEMBLYSCAN {
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::assembly-scan=0.4.1" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/assembly-scan:0.4.1--pyhdfd78af_0' :
-        'quay.io/biocontainers/assembly-scan:0.4.1--pyhdfd78af_0' }"
+    def container_image = "assembly-scan:0.4.1--pyhdfd78af_0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(assembly)

modules/nf-core/ataqv/ataqv/main.nf

@@ -3,9 +3,8 @@ process ATAQV_ATAQV {
     label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ataqv:1.3.0--py39hccc85d7_2' :
-        'quay.io/biocontainers/ataqv:1.3.0--py39hccc85d7_2' }"
+    def container_image = "ataqv:1.3.0--py39hccc85d7_2"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(bam), path(bai), path(peak_file)

modules/nf-core/ataqv/mkarv/main.nf

@@ -2,9 +2,8 @@ process ATAQV_MKARV {
     label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ataqv:1.3.0--py39hccc85d7_2':
-        'quay.io/biocontainers/ataqv:1.3.0--py39hccc85d7_2' }"
+    def container_image = "ataqv:1.3.0--py39hccc85d7_2"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     path json

modules/nf-core/atlas/call/main.nf

@@ -3,9 +3,8 @@ process ATLAS_CALL {
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0':
-        'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }"
+    def container_image = "atlas:0.9.9--h082e891_0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(bam), path(bai), path(pmd), path(recal)
@@ -42,7 +41,6 @@ process ATLAS_CALL {
         method=${method} \\
         $args
 
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         atlas: \$((atlas 2>&1) | grep Atlas | head -n 1 | sed -e 's/^[ \t]*Atlas //')

modules/nf-core/atlas/pmd/main.nf

@@ -3,9 +3,8 @@ process ATLAS_PMD {
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0':
-        'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }"
+    def container_image = "atlas:0.9.9--h082e891_0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(bam), path(bai), path(pool_rg_txt)

modules/nf-core/atlas/recal/main.nf

@@ -3,9 +3,8 @@ process ATLAS_RECAL {
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0':
-        'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }"
+    def container_image = "atlas:0.9.9--h082e891_0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(bam), path(bai), path(empiric), path(readgroups)

modules/nf-core/atlas/splitmerge/main.nf

@@ -3,9 +3,8 @@ process ATLAS_SPLITMERGE {
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0':
-        'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }"
+    def container_image = "atlas:0.9.9--h082e891_0"
+    container [ params.container_registry ?: 'quay.io/biocontainers' , container_image ].join('/')
 
     input:
     tuple val(meta), path(bam), path(bai), path(read_group_settings), path(blacklist)