Add support to Apple container in tools

.github/snapshots/apple_container.nf.test.snap

@@ -0,0 +1,114 @@
+{
+    "-profile test": {
+        "content": [
+            {
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "Workflow": {
+                    "my-prefix/testpipeline": "v1.0.0dev"
+                }
+            },
+            [
+                "fastqc",
+                "fastqc/SAMPLE1_PE_1_fastqc.html",
+                "fastqc/SAMPLE1_PE_1_fastqc.zip",
+                "fastqc/SAMPLE1_PE_2_fastqc.html",
+                "fastqc/SAMPLE1_PE_2_fastqc.zip",
+                "fastqc/SAMPLE2_PE_1_fastqc.html",
+                "fastqc/SAMPLE2_PE_1_fastqc.zip",
+                "fastqc/SAMPLE2_PE_2_fastqc.html",
+                "fastqc/SAMPLE2_PE_2_fastqc.zip",
+                "fastqc/SAMPLE3_SE_1_fastqc.html",
+                "fastqc/SAMPLE3_SE_1_fastqc.zip",
+                "fastqc/SAMPLE3_SE_2_fastqc.html",
+                "fastqc/SAMPLE3_SE_2_fastqc.zip",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_data/fastqc-status-check-heatmap.txt",
+                "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
+                "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
+                "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
+                "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
+                "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt",
+                "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
+                "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
+                "multiqc/multiqc_data/multiqc.log",
+                "multiqc/multiqc_data/multiqc.parquet",
+                "multiqc/multiqc_data/multiqc_citations.txt",
+                "multiqc/multiqc_data/multiqc_data.json",
+                "multiqc/multiqc_data/multiqc_fastqc.txt",
+                "multiqc/multiqc_data/multiqc_general_stats.txt",
+                "multiqc/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/multiqc_data/multiqc_sources.txt",
+                "multiqc/multiqc_plots",
+                "multiqc/multiqc_plots/pdf",
+                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/multiqc_plots/png",
+                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
+                "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/multiqc_plots/svg",
+                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
+                "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
+                "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
+                "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/testpipeline_software_mqc_versions.yml"
+            ],
+            [
+                "fastqc-status-check-heatmap.txt:md5,0f1975c565a16bf09be08a05c204ded7",
+                "fastqc_overrepresented_sequences_plot.txt:md5,4b23cea39c4e23deef6b97810bc1ee46",
+                "fastqc_per_base_n_content_plot.txt:md5,037692101c0130c72493d3bbfa3afac1",
+                "fastqc_per_base_sequence_quality_plot.txt:md5,bfe735f3e31befe13bdf6761bb297d6e",
+                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,7108d19c46ef7883e864ba274c457d2e",
+                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,23f527c80a148e4f34e5a43f6e520a90",
+                "fastqc_per_sequence_quality_scores_plot.txt:md5,a0cc0e6df7bfb05257da1cfc88b13c50",
+                "fastqc_sequence_counts_plot.txt:md5,c6e4e1588e6765fe8df27812a1322fbd",
+                "fastqc_sequence_duplication_levels_plot.txt:md5,3cde2db4033f6c64648976d1174db925",
+                "fastqc_sequence_length_distribution_plot.txt:md5,e82b9b14a7e24c0c5f27af97cebb6870",
+                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+                "multiqc_fastqc.txt:md5,1a41c2158adc9947bff9232962f70110",
+                "multiqc_general_stats.txt:md5,0b54e4e764665bd57fe0f95216744a78"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2025-06-16T14:29:10.076573"
+    }
+}

.github/workflows/codspeed.yml

@@ -39,7 +39,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
         with:
-          version: ${{ github.event.inputs.nextflow-version || matrix.nextflow-version }}
+          version: "25.10.4"
 
       - name: Install uv
         uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0

nf_core/__main__.py

@@ -342,7 +342,7 @@ def command_pipelines_lint(
 @click.option(
     "-s",
     "--container-system",
-    type=click.Choice(["none", "singularity", "docker", "apptainer"]),
+    type=click.Choice(["none", "singularity", "docker", "apptainer", "appleContainer"]),
     help="Download container images of required software.",
 )
 @click.option(
@@ -1303,7 +1303,7 @@ def command_modules_create(
 )
 @click.option(
     "--profile",
-    type=click.Choice(["docker", "singularity", "conda"]),
+    type=click.Choice(["docker", "singularity", "conda", "appleContainer", "appleContainerWave"]),
     default=None,
     help="Run tests with a specific profile",
 )
@@ -1665,7 +1665,7 @@ def command_subworkflows_create(ctx, subworkflow, directory, author, force):
 )
 @click.option(
     "--profile",
-    type=click.Choice(["docker", "singularity", "conda"]),
+    type=click.Choice(["docker", "singularity", "conda", "appleContainer", "appleContainerWave"]),
     default=None,
     help="Run tests with a specific profile",
 )

nf_core/components/components_test.py

@@ -145,10 +145,16 @@ def check_inputs(self) -> None:
                     "type": "list",
                     "name": "profile",
                     "message": "Choose container software to run the test with",
-                    "choices": ["Docker", "Singularity", "Conda"],
+                    "choices": ["Docker", "Singularity", "Conda", "Apple Container", "Apple Container (Wave/arm64)"],
                 }
                 answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcore_question_style)
-                profile = answer["profile"].lower()
+                profile = answer["profile"]
+                # Map display names to Nextflow profile names
+                profile_map = {
+                    "Apple Container": "appleContainer",
+                    "Apple Container (Wave/arm64)": "appleContainerWave",
+                }
+                profile = profile_map.get(profile, profile.lower())
                 os.environ["PROFILE"] = profile
 
     def display_nftest_output(self, nftest_out: bytes, nftest_err: bytes) -> None:

nf_core/pipeline-template/README.md

@@ -26,6 +26,7 @@
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
+[![run with apple container](https://img.shields.io/badge/run%20with-apple%20container-000000.svg?labelColor=000000&logo=apple)](https://github.com/apple/container)
 [![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/{{ name }})
 
 {% endif -%}

nf_core/pipeline-template/docs/usage.md

@@ -164,10 +164,12 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
   - A generic configuration profile to be used with [Charliecloud](https://charliecloud.io/)
 - `apptainer`
   - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
+- `appleContainer`
+  - A generic configuration profile to be used with [Apple container](https://github.com/apple/container) on macOS (Apple silicon)
 - `wave`
   - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow `24.03.0-edge` or later).
 - `conda`
-  - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
+  - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, or Apple container.
 
 ### `-resume`
 

nf_core/pipeline-template/nextflow.config

@@ -51,6 +51,14 @@ params {
     {%- if test_config %}
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'{% endif %}
     trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+    {%- if apple_container %}
+
+    // Apple Container options
+    // When true, the appleContainer profile emulates amd64 images with Rosetta
+    // (faster) instead of the default plain amd64 emulation. Requires Rosetta
+    // installed in the host OS.
+    apple_rosetta                = false
+    {%- endif %}
     {%- if nf_core_configs %}
 
     // Config options
@@ -107,8 +115,9 @@ profiles {
         podman.enabled          = false
         shifter.enabled         = false
         charliecloud.enabled    = false
-        conda.channels          = ['conda-forge', 'bioconda']
         apptainer.enabled       = false
+        appleContainer.enabled  = false
+        conda.channels          = ['conda-forge', 'bioconda']
     }
     mamba {
         conda.enabled           = true
@@ -119,6 +128,7 @@ profiles {
         shifter.enabled         = false
         charliecloud.enabled    = false
         apptainer.enabled       = false
+        appleContainer.enabled  = false
     }
     docker {
         docker.enabled          = true
@@ -128,6 +138,7 @@ profiles {
         shifter.enabled         = false
         charliecloud.enabled    = false
         apptainer.enabled       = false
+        appleContainer.enabled  = false
         docker.runOptions       = '-u $(id -u):$(id -g)'
     }
     arm64 {
@@ -153,6 +164,7 @@ profiles {
         shifter.enabled         = false
         charliecloud.enabled    = false
         apptainer.enabled       = false
+        appleContainer.enabled  = false
     }
     podman {
         podman.enabled          = true
@@ -162,6 +174,7 @@ profiles {
         shifter.enabled         = false
         charliecloud.enabled    = false
         apptainer.enabled       = false
+        appleContainer.enabled  = false
     }
     shifter {
         shifter.enabled         = true
@@ -171,6 +184,7 @@ profiles {
         podman.enabled          = false
         charliecloud.enabled    = false
         apptainer.enabled       = false
+        appleContainer.enabled  = false
     }
     charliecloud {
         charliecloud.enabled    = true
@@ -180,6 +194,7 @@ profiles {
         podman.enabled          = false
         shifter.enabled         = false
         apptainer.enabled       = false
+        appleContainer.enabled  = false
     }
     apptainer {
         apptainer.enabled       = true
@@ -190,6 +205,50 @@ profiles {
         podman.enabled          = false
         shifter.enabled         = false
         charliecloud.enabled    = false
+        appleContainer.enabled  = false
+    }
+    appleContainer {
+        appleContainer.enabled  = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
+        // Apple Container runs natively on Apple Silicon (arm64), but like
+        // Docker it can also run amd64 images via emulation. Since most nf-core
+        // modules ship amd64 container images, emulate amd64 by default so
+        // standard pipelines run without any Wave dependency. Set
+        // `--apple_rosetta` to use faster Rosetta emulation (requires Rosetta
+        // installed in the Apple Container VM).
+        process.arch              = 'linux/amd64'
+        appleContainer.runOptions = params.apple_rosetta ? '--platform linux/amd64 --rosetta' : '--platform linux/amd64'
+    }
+    appleContainerWave {
+        // Self-contained Apple Container + Wave profile: provision native arm64
+        // images from conda via Wave instead of emulating amd64. Usable on its
+        // own (`-profile appleContainerWave`, e.g. with
+        // `nf-core modules test --profile appleContainer`-style single-profile
+        // callers) or composed after appleContainer
+        // (`-profile appleContainer,appleContainerWave`). Faster per task when
+        // an arm64 build exists, but only works for tools with an arm64 (conda
+        // linux-aarch64 / multi-arch) build available, and pushes frozen images
+        // to a registry (set TOWER_ACCESS_TOKEN for durable, reproducible
+        // builds).
+        appleContainer.enabled    = true
+        conda.enabled             = false
+        docker.enabled            = false
+        singularity.enabled       = false
+        podman.enabled            = false
+        shifter.enabled           = false
+        charliecloud.enabled      = false
+        apptainer.enabled         = false
+        process.arch              = 'arm64'
+        appleContainer.runOptions = ''
+        wave.enabled              = true
+        wave.freeze               = true
+        wave.strategy             = 'conda,container'
     }
     wave {
         apptainer.ociAutoPull   = true
@@ -236,14 +295,15 @@ includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !pa
 // includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/{{ short_name }}.config" : "/dev/null"
 {%- endif %}
 
-// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
-// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
+// Set default registry for Apptainer, Docker, Podman, Charliecloud, Singularity and Apple container independent of -profile
+// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity / Apple container are enabled
 // Set to your registry if you have a mirror of containers
-apptainer.registry    = 'quay.io'
-docker.registry       = 'quay.io'
-podman.registry       = 'quay.io'
-singularity.registry  = 'quay.io'
-charliecloud.registry = 'quay.io'
+apptainer.registry      = 'quay.io'
+appleContainer.registry = 'quay.io'
+docker.registry         = 'quay.io'
+podman.registry         = 'quay.io'
+singularity.registry    = 'quay.io'
+charliecloud.registry   = 'quay.io'
 
 {% if igenomes -%}
 // Load igenomes.config if required

nf_core/pipeline-template/nextflow_schema.json

@@ -226,7 +226,14 @@
                     "fa_icon": "far calendar",
                     "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
                     "hidden": true
-                }{% if nf_schema %},
+                }{% if apple_container %},
+                "apple_rosetta": {
+                    "type": "boolean",
+                    "fa_icon": "fab fa-apple",
+                    "description": "Use faster Rosetta amd64 emulation in the appleContainer profile instead of plain amd64 emulation.",
+                    "help_text": "Only applies to the `appleContainer` profile. When `true`, amd64 container images are emulated with Rosetta (faster) instead of the default plain amd64 emulation. Requires Rosetta to be installed in the Apple Container VM.",
+                    "hidden": true
+                }{% endif %}{% if nf_schema %},
                 "help": {
                     "type": ["boolean", "string"],
                     "description": "Display the help message."

nf_core/pipelines/containers_utils.py

@@ -17,6 +17,8 @@
     "singularity_oras_arm64": ["singularity", "linux/arm64", "name"],
     "singularity_https_amd64": ["singularity", "linux/amd64", "https"],
     "singularity_https_arm64": ["singularity", "linux/arm64", "https"],
+    "appleContainer_amd64": ["docker", "linux/amd64", "name"],
+    "appleContainer_arm64": ["docker", "linux/arm64", "name"],
     "conda_lock_files_amd64": ["conda", "linux/amd64", "lock_file"],
     "conda_lock_files_arm64": ["conda", "linux/arm64", "lock_file"],
 }