Removed quay.io from all docker containers

quay.io is now a pipeline-level default, so we remove it from all Docker
container references. This should still build pipelines as before.

CHANGELOG.md

@@ -15,6 +15,8 @@
 - Remove `.cff` files from `.editorconfig` [(#2145)[https://github.com/nf-core/tools/pull/2145]]
 - Simplify pipeline README ([#2186](https://github.com/nf-core/tools/issues/2186))
 - Added support for the apptainer container engine via `-profile apptainer`. ([#2244](https://github.com/nf-core/tools/issues/2244)) [Contributed by @jfy133]
+- Added config `docker.registry` to pipeline template for a configurable default container registry when using Docker containers. Defaults to `quay.io` ([#2133](https://github.com/nf-core/tools/pull/2133))
+- Removed `quay.io` from all module Docker container references as this is now supplied at pipeline level. ([#2249](https://github.com/nf-core/tools/pull/2249))
 
 ### Linting
 

README.md

@@ -386,7 +386,7 @@ The Singularity image download finds containers using two methods:
 2. It scrapes any files it finds with a `.nf` file extension in the workflow `modules` directory for lines
    that look like `container = "xxx"`. This is the typical method for DSL2 pipelines, which have one container per process.
 
-Some DSL2 modules have container addresses for docker (eg. `quay.io/biocontainers/fastqc:0.11.9--0`) and also URLs for direct downloads of a Singularity continaer (eg. `https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0`).
+Some DSL2 modules have container addresses for docker (eg. `biocontainers/fastqc:0.11.9--0`) and also URLs for direct downloads of a Singularity continaer (eg. `https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0`).
 Where both are found, the download URL is preferred.
 
 Once a full list of containers is found, they are processed in the following order:

nf_core/download.py

@@ -432,7 +432,7 @@ def find_container_images(self):
         Later DSL2:
             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' }"
 
         DSL1 / Special case DSL2:
             container "nfcore/cellranger:6.0.2"

nf_core/module-template/modules/main.nf

@@ -30,7 +30,7 @@ process {{ component_name_underscore|upper }} {
     conda "{{ bioconda if bioconda else 'YOUR-TOOL-HERE' }}"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         '{{ singularity_container if singularity_container else 'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE' }}':
-        '{{ docker_container if docker_container else 'quay.io/biocontainers/YOUR-TOOL-HERE' }}' }"
+        '{{ docker_container if docker_container else 'biocontainers/YOUR-TOOL-HERE' }}' }"
 
     input:
     {% if not_empty_template -%}

nf_core/modules/bump_versions.py

@@ -172,7 +172,7 @@ def bump_module_version(self, module):
 
             patterns = [
                 (bioconda_packages[0], f"'bioconda::{bioconda_tool_name}={last_ver}'"),
-                (rf"quay.io/biocontainers/{bioconda_tool_name}:[^'\"\s]+", docker_img),
+                (rf"biocontainers/{bioconda_tool_name}:[^'\"\s]+", docker_img),
                 (
                     rf"https://depot.galaxyproject.org/singularity/{bioconda_tool_name}:[^'\"\s]+",
                     singularity_img,

nf_core/modules/lint/main_nf.py

@@ -545,5 +545,9 @@ def _container_type(line):
         if url_match:
             return "singularity"
         return None
-    if line.startswith("biocontainers/") or line.startswith("quay.io/"):
+    if (
+        line.startswith("biocontainers/")
+        or line.startswith("quay.io/")
+        or (line.count("/") == 1 and line.count(":") == 1)
+    ):
         return "docker"

nf_core/pipeline-template/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

tests/utils.py

@@ -102,7 +102,7 @@ def mock_biocontainers_api_calls(rsps: responses.RequestsMock, module, version):
             },
             {
                 "image_type": "Docker",
-                "image_name": f"quay.io/biocontainers/{module}:{version}",
+                "image_name": f"biocontainers/{module}:{version}",
                 "updated": "2021-09-04T00:00:00Z",
             },
         ],