Data lineage
This guide shows how to get started with native provenance tracking, also known as data lineage, introduced in Nextflow 25.04.
Warning
Data lineage is an experimental feature. It may change in future releases.
Overview
The provenance or lineage of a data entity, such as a file or record, is the history of computations and intermediate data that produced the entity. Data lineage is useful for verifying the integrity and reproducibility of pipeline results.
Nextflow’s built-in data lineage, when enabled, tracks all of your workflow runs, task runs, and outputs in a single place as lineage records. You can then query these records from the command line, or use them in a Nextflow script. Every lineage record has a unique hash called a lineage ID (LID) by which it is accessed.
Enable data lineage
To get started, enable data lineage in your Nextflow configuraiton:
lineage.enabled = true
Optionally, set the location of the lineage store:
lineage.store.location = '.lineage'
It defaults to .lineage in the current directory.
Tip
Place these settings in ~/.nextflow/config to apply them globally.
See the lineage config scope for details.
Generate lineage metadata
Run a Nextflow pipeline to generate some lineage metadata. For example:
nextflow run rnaseq-nf -profile conda
This pipeline will execute several tasks and publish several output files, all of which will be recorded in the lineage store.
Explore lineage
Now that you have generated some lineage metadata, you can explore it from the command line using the lineage command.
First, use the list subcommand to list the workflow runs in the lineage store:
$ nextflow lineage list
TIMESTAMP RUN NAME SESSION ID LINEAGE ID
2025-05-09 13:28:30 CDT peaceful_blackwell 065bdc6b-89b4-42ee-92c1-2a5af37f2c50 lid://16b31030474f2e96c55f4940bca3ab64
The lineage ID (LID) is the unique identifier for the workflow run and the entrypoint for exploring the lineage.
Use the view subcommand to view the lineage record for the workflow run:
$ nextflow lineage view lid://16b31030474f2e96c55f4940bca3ab64
{
"type": "WorkflowRun",
"workflow": {
"scriptFiles": [
...
],
"repository": "https://github.com/nextflow-io/rnaseq-nf",
"commitId": "86165b8c81d43a1f57363964431395152e353e56"
},
"sessionId": "065bdc6b-89b4-42ee-92c1-2a5af37f2c50",
"name": "peaceful_blackwell",
"params": [
...
],
"config": {
...
}
}
Every workflow run is represented in the lineage store as a WorkflowRun record, which includes information such as the pipeline repository, revision, run name, parameters, and resolved config.
Note
The data model for every lineage record is defined in the Nextflow source code.
The output files of a workflow run can be accessed as lid://<workflow-run-hash>/<path>, where <path> is the file path relative to the workflow output directory.
Note
Files must be published to the workflow output directory as defined by the outputDir config option (or -output-dir command line option) in order to be recorded as workflow outputs in the lineage store.
List the output directory to see the available files:
$ find results
results
results/fastqc_ggal_gut_logs
results/fastqc_ggal_gut_logs/ggal_gut_1_fastqc.html
results/fastqc_ggal_gut_logs/ggal_gut_1_fastqc.zip
results/fastqc_ggal_gut_logs/ggal_gut_2_fastqc.html
results/fastqc_ggal_gut_logs/ggal_gut_2_fastqc.zip
results/multiqc_report.html
Now, use the workflow LID and relative path to view the lineage record for an output file:
$ nextflow lineage view lid://16b31030474f2e96c55f4940bca3ab64/multiqc_report.html
{
"type": "FileOutput",
"path": "/results/multiqc_report.html",
"checksum": {
"value": "03fd5ed150c7862e1fad5efd4f574a47",
"algorithm": "nextflow",
"mode": "standard"
},
"source": "lid://862df53160e07cd823c0c3960545e747/multiqc_report.html",
"workflowRun": "lid://16b31030474f2e96c55f4940bca3ab64",
"taskRun": null,
"size": 5079806,
"createdAt": "2025-05-09T13:27:34.576590545-05:00",
"modifiedAt": "2025-05-09T13:27:34.586590551-05:00",
"labels": null
}
Every output file is represented in the lineage store as a FileOutput record, which includes basic file information such as the real path, checksum, file size and created/modified timestamps. It also includes lineage information, such as the workflow run and task run that produced it.
Since this record is a workflow output, it is not linked directly to a task run, but rather to the original task output.
Any LID in a lineage record can itself be viewed, allowing you to traverse the lineage metadata interactively. Use the value of source to view the original task output:
$ nextflow lineage view lid://862df53160e07cd823c0c3960545e747/multiqc_report.html
{
"type": "FileOutput",
"path": "/work/86/2df53160e07cd823c0c3960545e747/multiqc_report.html",
"checksum": {
"value": "b14f5171a48ce5c22ea27d7b8e57b6c4",
"algorithm": "nextflow",
"mode": "standard"
},
"source": "lid://862df53160e07cd823c0c3960545e747",
"workflowRun": "lid://16b31030474f2e96c55f4940bca3ab64",
"taskRun": "lid://862df53160e07cd823c0c3960545e747",
"size": 5079806,
"createdAt": "2025-05-09T13:27:34.236590379-05:00",
"modifiedAt": "2025-05-09T13:27:34.246590383-05:00",
"labels": null
}
This record is the task output for the same file – it has a value for taskRun which is the same as its source.
View the lineage record for the task that produced this file:
$ nextflow lineage view lid://862df53160e07cd823c0c3960545e747
{
"type": "TaskRun",
"sessionId": "065bdc6b-89b4-42ee-92c1-2a5af37f2c50",
"name": "MULTIQC",
"codeChecksum": {
"value": "edf2e9f84cd3a18ee9259012b660f2dd",
"algorithm": "nextflow",
"mode": "standard"
},
"script": "\n cp multiqc/* .\n echo \"custom_logo: $PWD/nextflow_logo.png\" \u003e\u003e multiqc_config.yaml\n multiqc -n multiqc_report.html .\n ",
"input": [
{
"type": "path",
"name": "*",
"value": [
"lid://eff8846883b46c5a76f11e7e4480a6c8/ggal_gut",
"lid://2d8bd92c69f732605bc99941e60d5319/fastqc_ggal_gut_logs"
]
},
{
"type": "path",
"name": "config",
"value": [
{
"path": "https://github.com/nextflow-io/rnaseq-nf/tree/86165b8c81d43a1f57363964431395152e353e56/multiqc",
"checksum": {
"value": "2aac500cdfb292e961e678433e7dc3d8",
"algorithm": "nextflow",
"mode": "standard"
}
}
]
}
],
"container": null,
"conda": "file:///conda/env-4a436c230263dfdbbf4dddd0623505d1",
"spack": null,
"architecture": null,
"globalVars": {},
"binEntries": [],
"workflowRun": "lid://16b31030474f2e96c55f4940bca3ab64"
}
Every task run is represented in the lineage store as a TaskRun, which includes information such as the name, script, inputs, and software dependencies. From here, you can continue traversing through the file inputs to view upstream tasks.
Finally, use the render subcommand to render the entire lineage of the MULTIQC report as an HTML report:
$ nextflow lineage render lid://16b31030474f2e96c55f4940bca3ab64/multiqc_report.html
Rendered lineage graph for lid://16b31030474f2e96c55f4940bca3ab64/multiqc_report.html to lineage.html
Open the HTML report in a web browser to view the lineage graph.
Query lineage records
To find a lineage record, you normally have to know the LID of the record, or you have to know the LID of a downstream record (such as a workflow run) from which you can traverse to the desired record. However, you can also query the entire lineage store by fields, allowing you to quickly find relevant records and aggregate records from different runs.
Use the find subcommand to find all tasks executed by a workflow run:
$ nextflow lineage find type=TaskRun workflowRun=lid://16b31030474f2e96c55f4940bca3ab64
[
"lid://2d8bd92c69f732605bc99941e60d5319",
"lid://eff8846883b46c5a76f11e7e4480a6c8",
"lid://862df53160e07cd823c0c3960545e747",
"lid://6d3bff36bf2c3c14c2d383384621e8ca"
]
You can use any field defined the lineage data model.
Tip
Since the find and view subcommands always output JSON, you can use JSON processing tools such as jq to further query and transform results.
Compare two task runs
Since task run LIDs are based on the standard task hash, it is easy to compare two task runs in the lineage metadata. This is especially useful when a task is unexpectedly re-executed during a resumed run. As long as lineage is enabled for the initial and resumed runs, the two tasks can be compared without any additional runs.
This section builds on the previous rnaseq-nf example to demonstrate how to compare two task runs in the event of a cache invalidation.
First, modify the pipeline in a way that invalidates the cache, such as modifying the script of the MULTIQC process.
Resume the pipeline, which should re-execute the MULTIQC task:
$ nextflow run rnaseq-nf -profile conda -resume
...
[6d/3bff36] process > RNASEQ:INDEX (ggal_1_48850000_49020000) [100%] 1 of 1, cached: 1 ✔
[2d/8bd92c] process > RNASEQ:FASTQC (FASTQC on ggal_gut) [100%] 1 of 1, cached: 1 ✔
[ef/f88468] process > RNASEQ:QUANT (ggal_gut) [100%] 1 of 1, cached: 1 ✔
[94/33dda7] process > MULTIQC [100%] 1 of 1 ✔
Retrieve the hash of the MULTIQC run from the log file or work directory – in this case it is 9433dda73f2193491f9a26e3e23cd8a1.
Finally, compare the task hash of the initial run (taken from the original example) to that of the resumed run:
$ nextflow lineage diff lid://862df53160e07cd823c0c3960545e747 lid://9433dda73f2193491f9a26e3e23cd8a1
diff --git 862df53160e07cd823c0c3960545e747 9433dda73f2193491f9a26e3e23cd8a1
--- 862df53160e07cd823c0c3960545e747
+++ 9433dda73f2193491f9a26e3e23cd8a1
@@ -3,11 +3,11 @@
"sessionId": "065bdc6b-89b4-42ee-92c1-2a5af37f2c50",
"name": "MULTIQC",
"codeChecksum": {
- "value": "edf2e9f84cd3a18ee9259012b660f2dd",
+ "value": "9615a8da3a3f9e935cfc8e4042cdf5e0",
"algorithm": "nextflow",
"mode": "standard"
},
- "script": "\n cp multiqc/* .\n echo \"custom_logo: $PWD/nextflow_logo.png\" \u003e\u003e multiqc_config.yaml\n multiqc -n multiqc_report.html .\n ",
+ "script": "\n cp multiqc/* . # hello!\n echo \"custom_logo: $PWD/nextflow_logo.png\" \u003e\u003e multiqc_config.yaml\n multiqc -n multiqc_report.html .\n ",
"input": [
{
"type": "path",
@@ -38,5 +38,5 @@
"architecture": null,
"globalVars": {},
"binEntries": [],
- "workflowRun": "lid://16b31030474f2e96c55f4940bca3ab64"
+ "workflowRun": "lid://65044872aad36f97e42336b9ba0dee57"
}
Note the difference between the task scripts, highlighting the change that caused the task to be re-executed.
Use lineage with workflow outputs
Workflow outputs declared in the output block are also recorded in the lineage store. The output of a workflow run can be accessed as lid://<workflow-run-hash>#output.
Run the rnaseq-nf pipeline using the preview-25-04 branch, which uses the output block to publish outputs:
$ nextflow -r preview-25-04 -profile conda
View the workflow output in the lineage metadata:
$ nextflow lineage view lid://9410d13abeec617640b5fe9735ba12fc#output
[
{
"type": "Collection",
"name": "samples",
"value": "lid://9410d13abeec617640b5fe9735ba12fc/samples.json"
},
{
"type": "Path",
"name": "summary",
"value": "lid://9410d13abeec617640b5fe9735ba12fc/multiqc_report.html"
}
]
This view can be used to traverse output files directly instead of inferring LIDs from the workflow output directory.
See Workflow outputs for more information about the output block.
Use lineage in a Nextflow script
Since lineage IDs are valid URIs, output files in the lineage store can be accessed by their LID in a Nextflow script, like any other path. The LID path returns the real path as defined by the path field in the FileOutput record.
The following script uses the samples.json from the previous example as an input samplesheet:
channel.fromPath('lid://9410d13abeec617640b5fe9735ba12fc/samples.json')
.splitJson()
.view()
[id:gut, quant:/results/gut/quant, fastqc:/results/gut/fastqc]
The fromLineage channel factory can also be used to query lineage records in a similar manner as the find subcommand. See fromLineage for details.