From ec5d1659086f215bb7afda3d56df8122f599c87f Mon Sep 17 00:00:00 2001 From: delfiterradas Date: Tue, 6 Oct 2026 16:50:26 +0000 Subject: [PATCH 1/2] Use latest DOI --- README.md | 4 ++-- ro-crate-metadata.json | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index e5a8c65..6de979e 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ [![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) [![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) -[![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.23170286-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.23170286) +[![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) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![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/) [![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) @@ -96,7 +96,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations -If you use nf-core/datasync for your analysis, please cite it using the following doi: [10.5281/zenodo.23170286](https://doi.org/10.5281/zenodo.23170286) +If 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) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 8007824..1f130c2 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "Stable", "datePublished": "2026-10-06T12:16:42+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.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\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\n\n\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", + "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": [ { "@id": "main.nf" From 67f288a497bee40914ef91e3c3627e5c3a63f77e Mon Sep 17 00:00:00 2001 From: delfiterradas Date: Tue, 6 Oct 2026 17:08:31 +0000 Subject: [PATCH 2/2] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d0bef1f..7131f9c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [[#102](https://github.com/nf-core/datasync/pull/102)] - Use the DOI that will always resolve to the latest version ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila)). - [[#99](https://github.com/nf-core/datasync/pull/99)] - Bump pipeline's version and add zenodo DOI ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila)). ## v1.0.1 - 2026-10-02