Post-release version bump

.nf-core.yml

@@ -16,4 +16,4 @@ template:
   name: datasync
   org: nf-core
   outdir: .
-  version: 1.0.2
+  version: 1.1.0dev

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`

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/datasync/releases/tag/1.0.2" target="_blank">nf-core/datasync</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/datasync/1.0.2/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/datasync/tree/dev" target="_blank">nf-core/datasync</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/datasync/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-datasync-methods-description":
     order: -1000

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'
 }
 

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": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-datasync_logo_dark.png\">\n    <img alt=\"nf-core/datasync\" src=\"docs/images/nf-core-datasync_logo_light.png\">\n  </picture>\n</h1>\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 <VERSION> \\\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"
@@ -134,25 +134,25 @@
                     "@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"
                 }
             ],
             "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"
         },

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"

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"

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"