diff --git a/.nf-core.yml b/.nf-core.yml index 2adc69e..3e19c08 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -16,4 +16,4 @@ template: name: datasync org: nf-core outdir: . - version: 1.0.2 + version: 1.1.0dev diff --git a/CHANGELOG.md b/CHANGELOG.md index 7131f9c..a35aff5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v1.1.0dev + +### `Added` + +### `Fixed` + +### `Changed` + ## v1.0.2 - 2026-10-06 ### `Fixed` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 62af733..343407c 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-core/datasync analysis pipeline. For information about how to interpret these results, please see the documentation. + This report has been generated by the nf-core/datasync analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: "nf-core-datasync-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 1e6e875..8015929 100644 --- a/nextflow.config +++ b/nextflow.config @@ -293,7 +293,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'main' nextflowVersion = '!>=25.10.4' - version = '1.0.2' + version = '1.1.0dev' doi = '10.5281/zenodo.23104575' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 1f130c2..5491c86 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,8 +21,8 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "Stable", - "datePublished": "2026-10-06T12:16:42+00:00", + "creativeWorkStatus": "InProgress", + "datePublished": "2026-10-06T17:50:08+00:00", "description": "

\n \n \n \"nf-core/datasync\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/datasync)\n[![GitHub Actions CI Status](https://github.com/nf-core/datasync/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/datasync/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/datasync/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/datasync/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/datasync/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.23104575-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.23104575)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![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/nf-core/datasync)\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23datasync-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/datasync)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/datasync** is a Nextflow pipeline for copying files and directories between storage locations and documenting their integrity. For every row in an input samplesheet, the pipeline:\n\n1. validates the source against a supplied MD5 and/or SHA-256 checksum manifest using [`rclone checksum`](https://rclone.org/commands/rclone_checksum/);\n2. copies the source to the requested destination with [`rclone copy`](https://rclone.org/);\n3. compares the copied data with the source using [`rclone check`](https://rclone.org/commands/rclone_check/); and\n4. produces detailed `rclone` status files and a consolidated MultiQC report.\n\nSources and destinations may be local paths or object-storage URIs such as Amazon S3, S3-compatible storage, or Azure Blob Storage. HTTP(S) URLs are not currently supported for samplesheet `input` or `output_path` values.\n\nThe current tested use case for this pipeline is transfer between S3 buckets.\n\nPass an `rclone` configuration with `--rclone_config` whenever a source or destination URI needs credentials or provider settings. Samplesheet paths use local paths or standard URIs such as `s3://bucket/path`, not rclone's `remote:path` syntax. For non-S3 layouts, design and validate the provider-specific configuration using the upstream [rclone documentation](https://rclone.org/docs/).\n\n![nf-core/datasync metro map](docs/images/datasync_nf-metro.svg)\n\n## Quick start\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, see the [nf-core environment setup guide](https://nf-co.re/docs/get_started/environment_setup/overview). Nextflow 25.10.4 or later is required.\n\nTo explore the pipeline outputs before preparing your own data, run the bundled `test` profile with a container profile:\n\n```bash\nnextflow run nf-core/datasync \\\n -profile test,docker \\\n --outdir results\n```\n\nThe `test` profile supplies a small samplesheet and `rclone` configuration automatically. It also enables `--rclone_dry_run`, so no files are actually transferred. This makes it useful for exploring the `rclone/` output folders and `multiqc/multiqc_report.html`; remember that post-copy comparison reports describe whatever is already present at the destination because the dry run does not write transfer data.\n\nTo run the pipeline on your own data, create a samplesheet containing one transfer per row:\n\n```csv\nsample,input,output_path,checksum_md5,checksum_sha\nrun_001,/data/run_001,s3://archive/runs,/data/manifests/run_001_md5.tsv\nreference,/data/reference.fa,/data/references,,/data/manifests/reference_sha256.tsv\n```\n\nThen launch the pipeline using:\n\n```bash\nnextflow run nf-core/datasync \\\n -r \\\n -profile docker \\\n --input samplesheet.csv \\\n --outdir results \\\n --rclone_config /path/to/rclone.conf\n```\n\n`--rclone_config` is optional only when every source and destination is accessible without a configured rclone remote. See the [`rclone` configuration section](docs/usage.md#configuring-rclone-remotes) for the tested S3-to-S3 use case and guidance on adapting rclone configuration files for other providers. To preview copy operations without transferring data, add `--rclone_dry_run`; note that subsequent comparison reports will then describe the unchanged destination.\n\nSee the [usage documentation](docs/usage.md) for samplesheet rules, destination semantics, remote configuration, and reproducible execution. The complete generated parameter reference is available on the [nf-core pipeline page](https://nf-co.re/datasync/parameters).\n\n## Pipeline output\n\nResults are written below `--outdir`. See the [output documentation](docs/output.md) for file names and status-code interpretation.\n\n## Credits\n\nnf-core/datasync was originally written by Alexander Peltzer.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- Julian Schwab\n- Gregor Sturm\n- Antonia Saracco\n- Delfina Terradas\n- Anabella Trigila\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#datasync` channel](https://nfcore.slack.com/channels/datasync) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/datasync for your analysis, please cite it using the following doi: [10.5281/zenodo.23104575](https://doi.org/10.5281/zenodo.23104575)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { @@ -102,7 +102,7 @@ }, "mentions": [ { - "@id": "#020e9608-3914-422a-bc82-144ce9fcf788" + "@id": "#a1898170-5367-44b1-a17f-3f2ae57384e4" } ], "name": "nf-core/datasync" @@ -134,7 +134,7 @@ "@id": "https://orcid.org/0000-0002-6503-2180" }, { - "@id": "#9f94a892-c2e4-4dea-9fa4-4c8d4c709492" + "@id": "#02aa1545-1c97-4abe-bbcd-e349c0511507" }, { "@id": "https://orcid.org/0000-0001-9584-7842" @@ -142,17 +142,17 @@ ], "contributor": [ { - "@id": "#52614e4f-c318-438e-bc47-ff2a07d52931" + "@id": "#baea0247-f00c-48b6-b641-1111db4f8b11" }, { - "@id": "#370daf34-3791-4655-8ade-5a7e148f585c" + "@id": "#17078e79-a00d-4ef1-9ad7-0c08578cd5d7" }, { - "@id": "#cd23cb4e-3f99-4877-994f-af3ce3ea2d28" + "@id": "#e94e34fd-eefd-4a85-9982-0dd3d93fabe7" } ], "dateCreated": "", - "dateModified": "2026-10-06T12:16:42Z", + "dateModified": "2026-10-06T17:50:08Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -172,10 +172,10 @@ }, "url": [ "https://github.com/nf-core/datasync", - "https://nf-co.re/datasync/1.0.2/" + "https://nf-co.re/datasync/dev/" ], "version": [ - "1.0.2" + "1.1.0dev" ] }, { @@ -191,11 +191,11 @@ "version": "!>=25.10.4" }, { - "@id": "#020e9608-3914-422a-bc82-144ce9fcf788", + "@id": "#a1898170-5367-44b1-a17f-3f2ae57384e4", "@type": "TestSuite", "instance": [ { - "@id": "#a91c423b-21ed-43f8-9102-0f637d86a978" + "@id": "#71dcedb8-3d40-4621-8f83-e8fb5c6f70d3" } ], "mainEntity": { @@ -204,7 +204,7 @@ "name": "Test suite for nf-core/datasync" }, { - "@id": "#a91c423b-21ed-43f8-9102-0f637d86a978", + "@id": "#71dcedb8-3d40-4621-8f83-e8fb5c6f70d3", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/datasync", "resource": "repos/nf-core/datasync/actions/workflows/nf-test.yml", @@ -344,25 +344,25 @@ "name": "Alexander Peltzer" }, { - "@id": "#52614e4f-c318-438e-bc47-ff2a07d52931", + "@id": "#baea0247-f00c-48b6-b641-1111db4f8b11", "@type": "Person", "email": "antonia.saracco@zs.com", "name": "Antonia Saracco" }, { - "@id": "#370daf34-3791-4655-8ade-5a7e148f585c", + "@id": "#17078e79-a00d-4ef1-9ad7-0c08578cd5d7", "@type": "Person", "email": "155591053+delfiterradas@users.noreply.github.com", "name": "Delfina Terradas" }, { - "@id": "#cd23cb4e-3f99-4877-994f-af3ce3ea2d28", + "@id": "#e94e34fd-eefd-4a85-9982-0dd3d93fabe7", "@type": "Person", "email": "18577080+atrigila@users.noreply.github.com", "name": "Anabella Trigila" }, { - "@id": "#9f94a892-c2e4-4dea-9fa4-4c8d4c709492", + "@id": "#02aa1545-1c97-4abe-bbcd-e349c0511507", "@type": "Person", "name": "Julian Schwab" }, diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index c7b93ba..4b82755 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -12,7 +12,7 @@ "rclone": "1.74.3-DEV" }, "Workflow": { - "nf-core/datasync": "v1.0.2" + "nf-core/datasync": "v1.1.0dev" } }, [ @@ -88,7 +88,7 @@ "benchmark_bed_checksum_MD5.missing_on_src.txt:lines,9" ] ], - "timestamp": "2026-10-06T12:21:56.462338211", + "timestamp": "2026-10-06T17:51:31.175325882", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/edge.nf.test.snap b/tests/edge.nf.test.snap index bcc7b55..a9ee204 100644 --- a/tests/edge.nf.test.snap +++ b/tests/edge.nf.test.snap @@ -12,7 +12,7 @@ "rclone": "1.74.3-DEV" }, "Workflow": { - "nf-core/datasync": "v1.0.2" + "nf-core/datasync": "v1.1.0dev" } }, [ @@ -123,7 +123,7 @@ "Illumina_annotation_sha_only_checksum_SHA256.exit_code.txt:lines,1" ] ], - "timestamp": "2026-10-06T12:22:37.58640014", + "timestamp": "2026-10-06T17:52:11.116267345", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -142,7 +142,7 @@ "rclone": "1.74.3-DEV" }, "Workflow": { - "nf-core/datasync": "v1.0.2" + "nf-core/datasync": "v1.1.0dev" } }, [ @@ -245,7 +245,7 @@ "Illumina_annotation_sha_only_checksum_SHA256.differ.txt:lines,15" ] ], - "timestamp": "2026-10-06T12:22:17.193039041", + "timestamp": "2026-10-06T17:51:50.915320643", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/main_full.nf.test.snap b/tests/main_full.nf.test.snap index a382900..13ae8e4 100644 --- a/tests/main_full.nf.test.snap +++ b/tests/main_full.nf.test.snap @@ -12,7 +12,7 @@ "rclone": "1.74.3-DEV" }, "Workflow": { - "nf-core/datasync": "v1.0.2" + "nf-core/datasync": "v1.1.0dev" } }, [ @@ -79,7 +79,7 @@ "demultiplex_checksum_SHA256.match.txt:lines,538" ] ], - "timestamp": "2026-10-06T12:24:05.982776133", + "timestamp": "2026-10-06T17:53:59.169348145", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4"