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

@@ -1,5 +1,49 @@
 # nf-core/tools: Changelog
 
+# v2.8dev
+
+### Template
+
+- Turn on automatic clean up of intermediate files in `work/` on successful pipeline completion in full-test config ([#2163](https://github.com/nf-core/tools/pull/2163)) [Contributed by @jfy133]
+- Add documentation to `usage.md` on how to use `params.yml` files, based on nf-core/ampliseq text ([#2173](https://github.com/nf-core/tools/pull/2173/)) [Contributed by @jfy133, @d4straub]
+- Make jobs automatically resubmit for a much wider range of exit codes (now `104` and `130..145`) ([#2170](https://github.com/nf-core/tools/pull/2170))
+- Add a stale GHA wich stale + close issues and stale PRs with specific labels ([#2183](https://github.com/nf-core/tools/pull/2183))
+- Remove problematic sniffer code in samplesheet_check.py that could give false positive 'missing header' errors ([https://github.com/nf-core/tools/pull/2194]) [Contributed by @Midnighter, @jfy133]
+- Consistent syntax for branch checks in PRs ([#2202](https://github.com/nf-core/tools/issues/2202))
+- Fixed minor Jinja2 templating bug that caused the PR template to miss a newline
+- Updated AWS tests to use newly moved `seqeralabs/action-tower-launch` instead of `nf-core/tower-action`
+- Remove `.cff` files from `.editorconfig` [(#2145)[https://github.com/nf-core/tools/pull/2145]]
+- 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.
+
+### Linting
+
+- Update modules lint test to fail if enable_conda is found ([#2213](https://github.com/nf-core/tools/pull/2213))
+- Read module lint configuration from `.nf-core.yml`, not `.nf-core-lint.yml` ([#2221](https://github.com/nf-core/tools/pull/2221))
+- `nf-core schema lint` now defaults to linting `nextflow_schema.json` if no filename is provided ([#2225](https://github.com/nf-core/tools/pull/2225))
+
+### Modules
+
+- Add an `--empty-template` option to create a module without TODO statements or examples ([#2175](https://github.com/nf-core/tools/pull/2175) & [#2177](https://github.com/nf-core/tools/pull/2177))
+- Removed the `nf-core modules mulled` command and all its code dependencies ([2199](https://github.com/nf-core/tools/pull/2199)).
+- Take into accout the provided `--git_remote` URL when linting all modules ([2243](https://github.com/nf-core/tools/pull/2243)).
+
+### Subworkflows
+
+- Fixing problem when a module included in a subworkflow had a name change from TOOL to TOOL/SUBTOOL ([#2177](https://github.com/nf-core/tools/pull/2177))
+- Fix `nf-core subworkflows test` not running subworkflow tests ([#2181](https://github.com/nf-core/tools/pull/2181))
+- Add tests for `nf-core subworkflows create-test-yml` ([#2219](https://github.com/nf-core/tools/pull/2219))
+
+### General
+
+- `nf-core modules/subworkflows info` now prints the include statement for the module/subworkflow ([#2182](https://github.com/nf-core/tools/pull/2182)).
+- Add a stale GHA wich stale + close issues and stale PRs with specific labels ([#2183](https://github.com/nf-core/tools/pull/2183))
+- update minimum version of rich to 13.3.1 ([#2185](https://github.com/nf-core/tools/pull/2185))
+- Add the Nextflow version to Gitpod container matching the minimal Nextflow version for nf-core (according to `nextflow.config`) ([#2196](https://github.com/nf-core/tools/pull/2196))
+- Use `nfcore/gitpod:dev` container in the dev branch ([#2196](https://github.com/nf-core/tools/pull/2196))
+- Replace requests_mock with responses in test mocks ([#2165](https://github.com/nf-core/tools/pull/2165)).
+- Add warning when installing a module from an `org_path` that exists in multiple remotes in `modules.json` ([#2228](https://github.com/nf-core/tools/pull/2228) [#2239](https://github.com/nf-core/tools/pull/2239)).
+
 ## [v2.7.2 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.2) - [2022-12-19]
 
 ### Template

README.md

@@ -385,7 +385,7 @@ 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

@@ -26,7 +26,7 @@ process {{ tool_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:
     // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"

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

@@ -528,5 +528,9 @@ 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

@@ -93,7 +93,7 @@ def mock_api_calls(mock, 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",
             },
         ],