Default registry to quay.io

.github/workflows/pytest-workflow.yml

@@ -207,7 +207,7 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@v2
         with:
-          name: logs-${{ matrix.profile }}
+          name: logs-${{ matrix.profile }}-${{ matrix.tags }}
           path: |
             /home/runner/pytest_workflow_*/*/.nextflow.log
             /home/runner/pytest_workflow_*/*/log.out

modules/nf-core/bases2fastq/main.nf

@@ -2,7 +2,7 @@ process BASES2FASTQ {
     tag "$meta.id"
     label 'process_high'
 
-    container "elembio/bases2fastq:1.1.0"
+    container "docker.io/elembio/bases2fastq:1.1.0"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

modules/nf-core/basicpy/main.nf

@@ -7,7 +7,7 @@ process BASICPY {
         exit 1, "Basicpy module does not support Conda. Please use Docker / Singularity instead."
     }
 
-    container "yfukai/basicpy-docker-mcmicro:0.2.1"
+    container "docker.io/yfukai/basicpy-docker-mcmicro:0.2.1"
 
     input:
     tuple val(meta), path(image)

modules/nf-core/bcl2fastq/main.nf

@@ -2,7 +2,7 @@ process BCL2FASTQ {
     tag {"$meta.lane" ? "$meta.id"+"."+"$meta.lane" : "$meta.id" }
     label 'process_high'
 
-    container "nfcore/bcl2fastq:2.20.0.422"
+    container "docker.io/nfcore/bcl2fastq:2.20.0.422"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

modules/nf-core/bclconvert/main.nf

@@ -2,7 +2,7 @@ process BCLCONVERT {
     tag {"$meta.lane" ? "$meta.id"+"."+"$meta.lane" : "$meta.id" }
     label 'process_high'
 
-    container "nfcore/bclconvert:4.0.3"
+    container "docker.io/nfcore/bclconvert:4.0.3"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

modules/nf-core/cat/fastq/main.nf

@@ -5,7 +5,7 @@ process CAT_FASTQ {
     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' }"
+        'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(reads, stageAs: "input*/*")

modules/nf-core/cellpose/main.nf

@@ -6,7 +6,7 @@ process CELLPOSE {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "I did not manage to create a cellpose module in Conda that works in all OSes. Please use Docker / Singularity / Podman instead."}
 
-    container "biocontainers/cellpose:2.1.1_cv2"
+    container "docker.io/biocontainers/cellpose:2.1.1_cv2"
 
     input:
     tuple val(meta), path(image)

modules/nf-core/cellranger/count/main.nf

@@ -2,7 +2,7 @@ process CELLRANGER_COUNT {
     tag "$meta.gem"
     label 'process_high'
 
-    container "nfcore/cellranger:7.1.0"
+    container "docker.io/nfcore/cellranger:7.1.0"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

modules/nf-core/cellranger/mkfastq/main.nf

@@ -2,7 +2,7 @@ process CELLRANGER_MKFASTQ {
     tag "mkfastq"
     label 'process_medium'
 
-    container "nfcore/cellrangermkfastq:7.1.0"
+    container "docker.io/nfcore/cellrangermkfastq:7.1.0"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

modules/nf-core/cellranger/mkgtf/main.nf

@@ -2,7 +2,7 @@ process CELLRANGER_MKGTF {
     tag "$gtf"
     label 'process_low'
 
-    container "nfcore/cellranger:7.1.0"
+    container "docker.io/nfcore/cellranger:7.1.0"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

modules/nf-core/cellranger/mkref/main.nf

@@ -2,7 +2,7 @@ process CELLRANGER_MKREF {
     tag "$fasta"
     label 'process_high'
 
-    container "nfcore/cellranger:7.1.0"
+    container "docker.io/nfcore/cellranger:7.1.0"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

modules/nf-core/coreograph/main.nf

@@ -2,7 +2,7 @@ process COREOGRAPH {
     tag "$meta.id"
     label 'process_single'
 
-    container "labsyspharm/unetcoreograph:2.2.9"
+    container "docker.io/labsyspharm/unetcoreograph:2.2.9"
 
     input:
     tuple val(meta), path(image)

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

@@ -5,7 +5,7 @@ process CUSTOM_TABULARTOGSEACLS {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(samples)

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

@@ -5,7 +5,7 @@ process CUSTOM_TABULARTOGSEAGCT {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(tabular)

modules/nf-core/deepcell/mesmer/main.nf

@@ -2,7 +2,7 @@ process DEEPCELL_MESMER {
     tag "$meta.id"
     label 'process_single'
 
-    container "vanvalenlab/deepcell-applications:0.4.1"
+    container "docker.io/vanvalenlab/deepcell-applications:0.4.1"
 
     input:
     tuple val(meta) , path(img)

modules/nf-core/deepvariant/main.nf

@@ -2,7 +2,7 @@ process DEEPVARIANT {
     tag "$meta.id"
     label 'process_medium'
 
-    container "google/deepvariant:1.4.0"
+    container "docker.io/google/deepvariant:1.4.0"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

modules/nf-core/eido/convert/main.nf

@@ -5,7 +5,7 @@ process EIDO_CONVERT {
     conda "conda-forge::eido=0.1.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/eido/0.1.9_cv1/eido_0.1.9_cv1.sif' :
-        'biocontainers/eido:0.1.9_cv1' }"
+        'docker.io/biocontainers/eido:0.1.9_cv1' }"
 
     input:
     path samplesheet
@@ -32,7 +32,7 @@ process EIDO_CONVERT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        eido: \$(echo \$(eido --version 2>&1) | sed 's/^.*eido //;s/ .*//' ))
+        eido: \$(echo \$(eido --version 2>&1) | sed 's/^.*eido //;s/ .*//' )
     END_VERSIONS
     """
 }

modules/nf-core/eido/validate/main.nf

@@ -5,7 +5,7 @@ process EIDO_VALIDATE {
     conda "conda-forge::eido=0.1.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/eido/0.1.9_cv2/eido_0.1.9_cv2.sif' :
-        'biocontainers/eido:0.1.9_cv2' }"
+        'docker.io/biocontainers/eido:0.1.9_cv2' }"
 
     input:
     path samplesheet

modules/nf-core/gatk4/applybqsrspark/main.nf

@@ -3,7 +3,7 @@ process GATK4_APPLYBQSR_SPARK {
     label 'process_low'
 
     conda "bioconda::gatk4=4.3.0.0 conda-forge::openjdk=8.0.312"
-    container 'broadinstitute/gatk:4.4.0.0'
+    container 'docker.io/broadinstitute/gatk:4.4.0.0'
 
     input:
     tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)

modules/nf-core/gatk4/baserecalibratorspark/main.nf

@@ -3,7 +3,7 @@ process GATK4_BASERECALIBRATOR_SPARK {
     label 'process_low'
 
     conda "bioconda::gatk4=4.4.0.0 conda-forge::openjdk=8.0.312"
-    container 'broadinstitute/gatk:4.4.0.0'
+    container 'docker.io/broadinstitute/gatk:4.4.0.0'
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)

modules/nf-core/gatk4/cnnscorevariants/main.nf

@@ -3,7 +3,7 @@ process GATK4_CNNSCOREVARIANTS {
     label 'process_low'
 
     //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
-    container "broadinstitute/gatk:4.4.0.0" //Biocontainers is missing a package
+    container "docker.io/broadinstitute/gatk:4.4.0.0" //Biocontainers is missing a package
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf

@@ -3,7 +3,7 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY {
     label 'process_single'
 
     //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
-    container "broadinstitute/gatk:4.4.0.0" //Biocontainers is missing a package
+    container "docker.io/broadinstitute/gatk:4.4.0.0" //Biocontainers is missing a package
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

modules/nf-core/gatk4/germlinecnvcaller/main.nf

@@ -3,7 +3,7 @@ process GATK4_GERMLINECNVCALLER {
     label 'process_single'
 
     //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
-    container "broadinstitute/gatk:4.4.0.0" //Biocontainers is missing a package
+    container "docker.io/broadinstitute/gatk:4.4.0.0" //Biocontainers is missing a package
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

modules/nf-core/gatk4/markduplicatesspark/main.nf

@@ -3,7 +3,7 @@ process GATK4_MARKDUPLICATES_SPARK {
     label 'process_high'
 
     conda "bioconda::gatk4=4.3.0.0 conda-forge::openjdk=8.0.312"
-    container 'broadinstitute/gatk:4.4.0.0'
+    container 'docker.io/broadinstitute/gatk:4.4.0.0'
 
     input:
     tuple val(meta), path(bam)

modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf

@@ -3,7 +3,7 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS {
     label 'process_single'
 
     //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
-    container "broadinstitute/gatk:4.4.0.0" //Biocontainers is missing a package
+    container "docker.io/broadinstitute/gatk:4.4.0.0" //Biocontainers is missing a package
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

modules/nf-core/gnu/sort/main.nf

@@ -5,7 +5,7 @@ process GNU_SORT {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-    'ubuntu:20.04' }"
+    'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(input)

modules/nf-core/gunzip/main.nf

@@ -5,7 +5,7 @@ process GUNZIP {
     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' }"
+        'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(archive)

modules/nf-core/igv/js/main.nf

@@ -6,7 +6,7 @@ process IGV_JS {
     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' }"
+        'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(alignment), path(index)

modules/nf-core/ilastik/multicut/main.nf

@@ -7,7 +7,7 @@ process ILASTIK_MULTICUT {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "ILASTIK_MULTICUT module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "biocontainers/ilastik:1.4.0_cv1"
+    container "docker.io/biocontainers/ilastik:1.4.0_cv1"
 
     input:
     tuple val(meta), path(h5)

modules/nf-core/ilastik/pixelclassification/main.nf

@@ -6,7 +6,7 @@ process ILASTIK_PIXELCLASSIFICATION {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "ILASTIK_PIXELCLASSIFICATION module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "biocontainers/ilastik:1.4.0_cv1"
+    container "docker.io/biocontainers/ilastik:1.4.0_cv1"
 
     input:
     tuple val(meta), path(input_img)

modules/nf-core/mcquant/main.nf

@@ -3,7 +3,7 @@ process MCQUANT {
     label 'process_single'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    container "labsyspharm/quantification:1.5.4"
+    container "docker.io/labsyspharm/quantification:1.5.4"
 
     input:
     tuple val(meta), path(image)

modules/nf-core/md5sum/main.nf

@@ -5,7 +5,7 @@ process MD5SUM {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(file)

modules/nf-core/scimap/mcmicro/main.nf

@@ -7,7 +7,7 @@ process SCIMAP_MCMICRO {
         exit 1, "Scimap module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
 
-    container "labsyspharm/scimap:0.22.0"
+    container "docker.io/labsyspharm/scimap:0.22.0"
 
     input:
     tuple val(meta), path(cellbyfeature)

modules/nf-core/sentieon/bwaindex/main.nf

@@ -8,7 +8,7 @@ process SENTIEON_BWAINDEX {
         exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
     }
 
-    container 'nfcore/sentieon:202112.06'
+    container 'docker.io/nfcore/sentieon:202112.06'
 
     input:
     tuple val(meta), path(fasta)

modules/nf-core/sentieon/bwamem/main.nf

@@ -10,7 +10,7 @@ process SENTIEON_BWAMEM {
         exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
     }
 
-    container 'nfcore/sentieon:202112.06'
+    container 'docker.io/nfcore/sentieon:202112.06'
 
     input:
     tuple val(meta), path(reads)

modules/nf-core/sentieon/dedup/main.nf

@@ -10,7 +10,7 @@ process SENTIEON_DEDUP {
         exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
     }
 
-    container 'nfcore/sentieon:202112.06'
+    container 'docker.io/nfcore/sentieon:202112.06'
 
     input:
     tuple val(meta), path(bam), path(bai)

modules/nf-core/sentieon/haplotyper/main.nf

@@ -10,7 +10,7 @@ process SENTIEON_HAPLOTYPER {
         exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
     }
 
-    container 'nfcore/sentieon:202112.06'
+    container 'docker.io/nfcore/sentieon:202112.06'
 
     input:
     val(emit_mode)

modules/nf-core/shasum/main.nf

@@ -5,7 +5,7 @@ process SHASUM {
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(file)

modules/nf-core/universc/README.md

@@ -45,10 +45,10 @@ process {
 
 ...
     withName: CELLRANGER_MKGTF {
-        container = "nfcore/universc:1.2.5.1"
+        container = "docker.io/nfcore/universc:1.2.5.1"
     }
     withName: CELLRANGER_MKREF{
-       container = "nfcore/universc:1.2.5.1"
+       container = "docker.io/nfcore/universc:1.2.5.1"
     }
 ...
 }
@@ -66,7 +66,7 @@ and for singularity use the `--writeable` parameter.
 These are set as default in universc/main.nf:
 
 ```
-    container "nfcore/universc:1.2.5.1"
+    container "docker.io/nfcore/universc:1.2.5.1"
     if (workflow.containerEngine == 'docker'){
         containerOptions = "--privileged"
     }

modules/nf-core/universc/main.nf

@@ -6,7 +6,7 @@ process UNIVERSC {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "UNIVERSC module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "nfcore/universc:1.2.5.1"
+    container "docker.io/nfcore/universc:1.2.5.1"
     if (workflow.containerEngine == 'docker'){
         containerOptions = "--privileged"
     }

modules/nf-core/untar/main.nf

@@ -5,7 +5,7 @@ process UNTAR {
     conda "conda-forge::sed=4.7 bioconda::grep=3.4 conda-forge::tar=1.34"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(archive)

modules/nf-core/untarfiles/main.nf

@@ -5,7 +5,7 @@ process UNTARFILES {
     conda "conda-forge::sed=4.7 bioconda::grep=3.4 conda-forge::tar=1.34"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(archive)