diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 4190c08..5a8075d 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -24,8 +24,6 @@ jobs:
- name: Launch workflow via Seqera Platform
uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2
- # Add full size test data (but still relatively small datasets for few samples)
- # on the `test_full.config` test runs with only one set of parameters
with:
workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index c11b24c..70658fa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,28 +9,9 @@ Initial release of nf-core/datasync, created with the [nf-core](https://nf-co.re
### `Added`
-- [[#87](https://github.com/nf-core/datasync/pull/87)] - Add local test profile ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila)).
-- [[#79](https://github.com/nf-core/datasync/pull/79)] - Add exit status for `RCLONE` modules in multiqc report ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila)).
-- [[#74](https://github.com/nf-core/datasync/pull/74)] - Implement warning and `--download` parameter when working with remote directories and SHA checksums ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila), [@apeltzer](https://github.com/apeltzer) and [@antoniasaracco](https://github.com/antoniasaracco)).
-- [[#67](https://github.com/nf-core/datasync/pull/67)] - Copy only files which are successfully validated ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila) and [@antoniasaracco](https://github.com/antoniasaracco)).
-- [[#57](https://github.com/nf-core/datasync/pull/57)] - Add nf-tests with edge cases([@atrigila](https://github.com/atrigila), review by [@delfiterradas](https://github.com/delfiterradas)).
-- [[#55](https://github.com/nf-core/datasync/pull/55)] - Add subdirectories with sample id to results. Improvements to MultiQC report (width of columns, sections and sub-section headers)colors to multiqc results and display first errors in tables ([@atrigila](https://github.com/atrigila), review by [@delfiterradas](https://github.com/delfiterradas)).
-- [[#54](https://github.com/nf-core/datasync/pull/54)] - Add colors to multiqc results and display first errors in tables ([@atrigila](https://github.com/atrigila), review by [@delfiterradas](https://github.com/delfiterradas)).
-- [[#31](https://github.com/nf-core/datasync/pull/31)] - Compute checksum for each input file ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila)).
-- [[#35](https://github.com/nf-core/datasync/pull/35)] - Compare generated checksum to given checksum in input and update test profiles ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila)).
-- [[#46](https://github.com/nf-core/datasync/pull/46)] - Import Rclone module from nf-core([@antoniasaracco](https://github.com/antoniasaracco), review by [@delfiterradas](https://github.com/delfiterradas)).
-- [[#41](https://github.com/nf-core/datasync/pull/41)] - Generate MultiQC Report with comparechecksum tables and input samplesheet ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila)).
-- [[#49](https://github.com/nf-core/datasync/pull/49)] - Install `RCLONE_CHECK` and `RCLONE_CHECKSUM` modules from nf-core ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila) and [@antoniasaracco](https://github.com/antoniasaracco)).
-- [[#59](https://github.com/nf-core/datasync/pull/59)] - Create pipeline documentation ([@antoniasaracco](https://github.com/antoniasaracco), review by [@atrigila](https://github.com/atrigila) and [@delfiterradas](https://github.com/delfiterradas)).
-
-### `Fixed`
-
-- [[#84](https://github.com/nf-core/datasync/pull/84)] - Update `RCLONE_` modules, enhance source and destination path handling, add local `create_filter_list` module and other small fixes ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila)).
-- [[#83](https://github.com/nf-core/datasync/pull/83)] - Add apptainer version to avoid error in CI test ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila)).
-- [[#78](https://github.com/nf-core/datasync/pull/78)] - Fixed linting issues reported by nf-core and Nextflow, and updated `rclone` modules and nf-tests to sort generated report files for deterministic snapshots ([@atrigila](https://github.com/atrigila), review by [@delfiterradas](https://github.com/delfiterradas) and [@antoniasaracco](https://github.com/antoniasaracco)).
-- [[#76](https://github.com/nf-core/datasync/pull/76)] - Remove `--one-way` from rclone/checksum confi ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila) and [@antoniasaracco](https://github.com/antoniasaracco)).
-- [[#73](https://github.com/nf-core/datasync/pull/73)] - Create tmp `files_to_copy.tx` avoiding error with write permissions in work directory ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila) and [@antoniasaracco](https://github.com/antoniasaracco)).
-
-### `Dependencies`
-
-### `Deprecated`
+- Samplesheet-driven copying of files and directories between local paths and rclone-supported object storage locations.
+- Validation of source data against supplied MD5 and SHA-256 checksum manifests before transfer.
+- The ability to copy only files that pass checksum validation, and to download remote files when SHA-256 verification is required.
+- Post-transfer comparison of copied data against the source, with detailed rclone status files for each sample.
+- A MultiQC report covering the input samplesheet, validation summary, checksum validation, and post-transfer checks.
+- A local test profile to explore the pipeline and its outputs.
diff --git a/README.md b/README.md
index 181e543..96f62ea 100644
--- a/README.md
+++ b/README.md
@@ -9,14 +9,12 @@
[](https://github.com/nf-core/datasync/actions/workflows/nf-test.yml)
[](https://github.com/nf-core/datasync/actions/workflows/linting.yml)[](https://nf-co.re/datasync/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)
[](https://www.nf-test.com)
-
[](https://www.nextflow.io/)
[](https://github.com/nf-core/tools/releases/tag/4.1.0)
[](https://docs.conda.io/en/latest/)
[](https://www.docker.com/)
[](https://sylabs.io/docs/)
[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/datasync)
-
[](https://nfcore.slack.com/channels/datasync)[](https://bsky.app/profile/nf-co.re)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)
## Introduction
@@ -34,7 +32,7 @@ The current tested use case for this pipeline is transfer between S3 buckets.
Pass 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/).
-
+
## Quick start
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index 6d48fd6..9abae2c 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,2 +1,2 @@
sample,input,output_path,checksum_md5
-sample,path/to/file,output_path,path/to/file
+sample,s3://foo/path/to/files/,output_path/data,path/to/checksum.md5
diff --git a/assets/samplesheet_full.csv b/assets/samplesheet_full.csv
deleted file mode 100644
index 9ed843e..0000000
--- a/assets/samplesheet_full.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-sample,input,checksum_md5,checksum_sha
-demultiplex,s3://nf-core-awsmegatests/demultiplex/results-fbec8e442f0599f8b74876e62263af05b9a41d33/,checksum_md5.tsv,checksum_sha.tsv
diff --git a/bin/create_test_files.sh b/bin/create_test_files.sh
deleted file mode 100644
index ddb0120..0000000
--- a/bin/create_test_files.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-# This script expects a single folder $1 with several subfolders that then need to be synchronized and checksummed to another location $2
-mkdir -p $1
-mkdir -p $2
-touch $1/DemuxDone #Note this needs to be configured as a pattern to look for in the pipeline configuration, otherwise this trigger won't work.
-touch $1/fake_file.fastq.gz
-touch $1/fake_file2.fastq.gz
-echo "Sync me to another place" > $1/SampleSheet.csv
diff --git a/conf/igenomes.config b/conf/igenomes.config
deleted file mode 100644
index e69de29..0000000
diff --git a/conf/igenomes_ignored.config b/conf/igenomes_ignored.config
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/images/datasync-metromap.png b/docs/images/datasync-metromap.png
deleted file mode 100644
index 108bbc0..0000000
Binary files a/docs/images/datasync-metromap.png and /dev/null differ
diff --git a/docs/images/datasync-nf-metro.mmd b/docs/images/datasync-nf-metro.mmd
new file mode 100644
index 0000000..c4558dd
--- /dev/null
+++ b/docs/images/datasync-nf-metro.mmd
@@ -0,0 +1,33 @@
+%%metro title: nf-core/datasync
+%%metro mode: dark
+%%metro style: nfcore
+%%metro diamond_style: symmetric
+%%metro line: main | Pipeline | #4CAF50
+
+%%metro file: ref_in | CSV | Input\nSamplesheet | banner
+%%metro file: reads_in | Config | Rclone\nConfig | banner
+%%metro file: report_out | HTML | Report | banner
+%%metro grid: datasync | 0,0
+
+graph LR
+ subgraph datasync [Datasync pipeline]
+ ref_in[Input]
+ reads_in[ ]
+ node1[Rclone\nChecksum]
+ node2[Create\nFilter List]
+ node3[Rclone\nCheck]
+ node4[Rclone\nCopy]
+ node5[MultiQC]
+ Rclone\nChecksum[Rclone\nChecksum]
+ ref_in -->|main| Rclone\nChecksum
+ reads_in -->|main| Rclone\nChecksum
+ report_out[Output]
+ ref_in -->|main| node1
+ reads_in -->|main| node1
+ node1 -->|main| node2
+ node2 -->|main| node4
+ node4 -->|main| node3
+ node3 -->|main| node5
+ node1 -->|main| node4
+ node5 -->|main| report_out
+ end
diff --git a/docs/images/datasync_nf-metro.svg b/docs/images/datasync_nf-metro.svg
new file mode 100644
index 0000000..62f95c3
--- /dev/null
+++ b/docs/images/datasync_nf-metro.svg
@@ -0,0 +1,98 @@
+
+
diff --git a/modules/local/create_filter_list/main.nf b/modules/local/create_filter_list/main.nf
index b82caed..1da22b7 100644
--- a/modules/local/create_filter_list/main.nf
+++ b/modules/local/create_filter_list/main.nf
@@ -7,12 +7,7 @@ process CREATE_FILTER_LIST {
output:
tuple val(meta), path('files_to_copy.txt')
- script:
- def content = common.join('\n')
-
- """
- cat > files_to_copy.txt <<'EOF'
-${content}
-EOF
- """
+ exec:
+ def outFile = task.workDir.resolve('files_to_copy.txt')
+ outFile.text = common.join('\n') + '\n'
}
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 738538e..a4a5f43 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -47,24 +47,24 @@
"exists": true,
"description": "Path to the rclone config file used for cloud storage authentication.",
"help_text": "Provide an rclone config file to support cloud providers such as AWS S3 or Azure Blob Storage. This file is loaded by rclone when copying data.",
- "fa_icon": "fas fa-file"
+ "fa_icon": "fas fa-cog"
},
"rclone_dry_run": {
"type": "boolean",
"description": "Perform a dry run of the rclone copy command.",
- "fa_icon": "fas fa-eye",
+ "fa_icon": "fas fa-forward",
"help_text": "If set, the pipeline will not actually copy any files to the destination. Instead, it will print out what would have been copied. This is useful for testing and debugging."
},
"copy_matching_only": {
"type": "boolean",
"description": "Only copy files that matched their provided input checksums.",
- "fa_icon": "fas fa-eye",
+ "fa_icon": "fas fa-copy",
"help_text": "If set, the pipeline will only copy files that were correctly validated and will skip any file that did not match their input checksum."
},
"download": {
"type": "boolean",
"description": "Download remote files for sha256 checksum verification in `RCLONE_CHECKSUM`.",
- "fa_icon": "fas fa-eye",
+ "fa_icon": "fas fa-cloud-download-alt",
"help_text": "If set, `RCLONE_CHECKSUM` will download remote files for any sample for which a SHA256 file was provided."
}
}
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 8ca15e3..919556e 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -23,7 +23,7 @@
"@type": "Dataset",
"creativeWorkStatus": "Stable",
"datePublished": "2026-09-08T15:38:46+00:00",
- "description": "
\n \n \n \n \n
\n\n[](https://github.com/codespaces/new/nf-core/datasync)\n[](https://github.com/nf-core/datasync/actions/workflows/nf-test.yml)\n[](https://github.com/nf-core/datasync/actions/workflows/linting.yml)[](https://nf-co.re/datasync/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://github.com/nf-core/tools/releases/tag/4.1.0)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/datasync)\n\n[](https://nfcore.slack.com/channels/datasync)[](https://bsky.app/profile/nf-co.re)[](https://mstdn.science/@nf_core)[](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\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 \n \n
\n\n[](https://github.com/codespaces/new/nf-core/datasync)\n[](https://github.com/nf-core/datasync/actions/workflows/nf-test.yml)\n[](https://github.com/nf-core/datasync/actions/workflows/linting.yml)[](https://nf-co.re/datasync/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://github.com/nf-core/tools/releases/tag/4.1.0)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/datasync)\n\n[](https://nfcore.slack.com/channels/datasync)[](https://bsky.app/profile/nf-co.re)[](https://mstdn.science/@nf_core)[](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\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",
"hasPart": [
{
"@id": "main.nf"
diff --git a/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf b/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf
index dca6fc9..2f42376 100644
--- a/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf
@@ -11,6 +11,7 @@
include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin'
include { paramsSummaryMap } from 'plugin/nf-schema'
include { samplesheetToList } from 'plugin/nf-schema'
+include { paramsHelp } from 'plugin/nf-schema'
include { completionEmail } from '../../nf-core/utils_nfcore_pipeline'
include { completionSummary } from '../../nf-core/utils_nfcore_pipeline'
include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline'
![\"nf-core/datasync\"](\"docs/images/nf-core-datasync_logo_dark.png\"){kind=logo}
\n