Redun

Here, we’ll see how to track redun workflows with lamindb.

Note

This guide is based on github.com/ricomnl/bioinformatics-pipeline-tutorial.

Amend the workflow

Here is how to instrument a redun workflow for tracking with lamindb:

1. Add ln.track() to the main() task (see on GitHub)

2. Register desired output files or folders by creating artifacts for them (see on GitHub):

   ln.Artifact(output_path, key="data/results.tar.gz").save()
   

3. Add a finish() task that calls ln.finish() (see on GitHub)

4. Optionally cache/stage input files (see on GitHub)

Why not use @ln.flow() for main()?

Because main() in redun is typically a scheduler/executor task rather than a task that performs the actual computation. ln.flow() would then just track the execution time of scheduling, and not an actual compute run.

If one wanted to use @ln.flow() it’s advisable to wrap the scheduling main() task:

@ln.flow()
def run_pipeline(...):
    scheduler = Scheduler()
    result = scheduler.run(main(...))  # run the main task
    ln.Artifact(result.path, key="data/results.tgz").save()
    return result

Run redun

Let’s see what the input files are:

ls ./fasta

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KLF4.fasta
MYC.fasta
PO5F1.fasta
SOX2.fasta

Create a lamindb test instance:

# pip install lamindb redun git+http://github.com/laminlabs/redun-lamin-fasta
lamin init --storage ./test-redun-lamin

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→ initialized database testuser1/test-redun-lamin in /home/runner/work/redun-lamin/redun-

lamin/docs

Register each input file individually as an artifact:

import lamindb as ln
import json

ln.Artifact.from_dir("./fasta").save()

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→ connected lamindb: testuser1/test-redun-lamin

! folder is outside existing storage location, will copy files from ./fasta to /home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/fasta

! no run & transform got linked, call `ln.track()` & re-run

! no run & transform got linked, call `ln.track()` & re-run

! no run & transform got linked, call `ln.track()` & re-run

! no run & transform got linked, call `ln.track()` & re-run

SQLRecordList([Artifact(uid='2xfEH3O2SzsCOmtJ0000', key='fasta/KLF4.fasta', description=None, suffix='.fasta', kind=None, otype=None, size=609, hash='LyuoYkWs4SgYcH7P7JLJtA', n_files=None, n_observations=None, extra_data=None, branch_id=1, created_on_id=1, space_id=1, storage_id=1, run_id=None, schema_id=None, created_by_id=1, created_at=2026-10-28 08:23:11 UTC, is_locked=False, version_tag=None, is_latest=True),
               Artifact(uid='A8dVi54KTbWg5SBB0000', key='fasta/MYC.fasta', description=None, suffix='.fasta', kind=None, otype=None, size=536, hash='WGbEtzPw-3bQEGcngO_pHQ', n_files=None, n_observations=None, extra_data=None, branch_id=1, created_on_id=1, space_id=1, storage_id=1, run_id=None, schema_id=None, created_by_id=1, created_at=2026-10-28 08:23:11 UTC, is_locked=False, version_tag=None, is_latest=True),
               Artifact(uid='u9ygeSJCACe8CTda0000', key='fasta/PO5F1.fasta', description=None, suffix='.fasta', kind=None, otype=None, size=477, hash='-7iJgveFO9ia0wE1bqVu6g', n_files=None, n_observations=None, extra_data=None, branch_id=1, created_on_id=1, space_id=1, storage_id=1, run_id=None, schema_id=None, created_by_id=1, created_at=2026-10-28 08:23:11 UTC, is_locked=False, version_tag=None, is_latest=True),
               Artifact(uid='GusEh1BzxzeKt2nl0000', key='fasta/SOX2.fasta', description=None, suffix='.fasta', kind=None, otype=None, size=414, hash='C5q_yaFXGk4SAEpfdqBwnQ', n_files=None, n_observations=None, extra_data=None, branch_id=1, created_on_id=1, space_id=1, storage_id=1, run_id=None, schema_id=None, created_by_id=1, created_at=2026-10-28 08:23:11 UTC, is_locked=False, version_tag=None, is_latest=True)])

Run the redun workflow:

redun run workflow.py main --input-dir ./fasta --tag run=test-run  1> run_logs.txt 2>run_logs.txt

Inspect the logs:

cat run_logs.txt

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→ connected lamindb: testuser1/test-redun-lamin
→ script invoked with: run wor

kflow.py main --input-dir ./fasta --tag run=test-run
→ created Transform('CTEut9YSBTZz000

0', key='workflow.py'), started new Run('kmKJaSrMZFQTrZ7e') at 2026-10-28 08:23:20 UTC
• 

tip: to identify the script across renames, pass the uid: ln.track("CTEut9YSBTZz")
File(path=/home/r

unner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=24912653)
cs_pipelin

e_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/d

ocs/test-redun-lamin/.lamindb/2xfEH3O2SzsCOmtJ0000.fasta, hash=3c6a0cd5), enzyme_regex='[KR]', misse

d_cleavages=0, min_length=4, max_length=75) on default
[redun] Run    Job d54eb388:  bioinformatics_

pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-

lamin/docs/test-redun-lamin/.lamindb/A8dVi54KTbWg5SBB0000.fasta, hash=821e187c), enzyme_regex='[KR]'

, missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run    Job fd881f0c:  bioinfor

matics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin

/redun-lamin/docs/test-redun-lamin/.lamindb/u9ygeSJCACe8CTda0000.fasta, hash=4b977f99), enzyme_regex

='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run    Job 66178b1a:  b

ioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redu

n-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/GusEh1BzxzeKt2nl0000.fasta, hash=93453059), enzym

e_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run    Job 3fd8b

7f5:  bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner

/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/2xfEH3O2SzsCOmtJ0000.fasta, hash=3c6a0c

d5), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/2

xfEH3O2SzsCOmtJ0000.peptides.txt, hash=6b12393c), amino_acid='C') on default
[redun] Run    Job 56c1

6302:  bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runne

r/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/A8dVi54KTbWg5SBB0000.fasta, hash=821e1

87c), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/

A8dVi54KTbWg5SBB0000.peptides.txt, hash=baa7462b), amino_acid='C') on default
[redun] Run    Job 118

f78e1:  bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runn

er/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/u9ygeSJCACe8CTda0000.fasta, hash=4b97

7f99), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data

/u9ygeSJCACe8CTda0000.peptides.txt, hash=46584b09), amino_acid='C') on default
[redun] Run    Job eb

fc3e00:  bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/run

ner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/GusEh1BzxzeKt2nl0000.fasta, hash=934

53059), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/dat

a/GusEh1BzxzeKt2nl0000.peptides.txt, hash=499543b2), amino_acid='C') on default
[redun] Run    Job f

beebdd5:  bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/wo

rk/redun-lamin/redun-lamin/docs/test-redun-lamin/data/2xfEH3O2SzsCOmtJ0000.count.tsv, hash=cd7d91fd)

) on default
[redun] Run    Job 35df5a68:  bioinformatics_pipeline_tutorial.lib.plot_count_task(inpu

t_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/A8dVi54KTbWg5

SBB0000.count.tsv, hash=8b3d9d0a)) on default
[redun] Run    Job 1b3f9288:  bioinformatics_pipeline_

tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/te

st-redun-lamin/data/u9ygeSJCACe8CTda0000.count.tsv, hash=4d4c404b)) on default
[redun] Run    Job 08

d95fc4:  bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/wor

k/redun-lamin/redun-lamin/docs/test-redun-lamin/data/GusEh1BzxzeKt2nl0000.count.tsv, hash=b2a8e3b5))

 on default
[redun] Run    Job 0c98f443:  bioinformatics_pipeline_tutorial.lib.get_report_task(input

_counts=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/2xfEH3O2SzsC

OmtJ0000.count.tsv, hash=cd7d91fd), File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-re

dun-l...) on default
[redun] Run    Job 797f27e5:  bioinformatics_pipeline_tutorial.lib.archive_resu

lts_task(inputs_plots=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/dat

a/2xfEH3O2SzsCOmtJ0000.plot.png, hash=ed7c4ed5), File(path=/home/runner/work/redun-lamin/redun-lamin

/docs/test-redun-la..., input_report=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-r

edun-lamin/data/protein_report.tsv, hash=f02868c2)) on default
[redun] Run    Job ffab6367:  redun_l

amin_fasta.finish(results_archive=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redu

n-lamin/data/results.tgz, hash=24912653)) on default
[redun] 
[redun] | JOB STATUS 2026/10/28 08:23:

34
[redun] | TASK                                                        PENDING RUNNING  FAILED  CA

CHED    DONE   TOTAL
[redun] | 
[redun] | ALL                                                       

        0       0       0       0      16      16
[redun] | bioinformatics_pipeline_tutorial.lib.arc

hive_results_task         0       0       0       0       1       1
[redun] | bioinformatics_pipelin

e_tutorial.lib.count_amino_acids_task       0       0       0       0       4       4
[redun] | bioi

nformatics_pipeline_tutorial.lib.digest_protein_task          0       0       0       0       4     

  4
[redun] | bioinformatics_pipeline_tutorial.lib.get_report_task              0       0       0   

    0       1       1
[redun] | bioinformatics_pipeline_tutorial.lib.plot_count_task              0 

      0       0       0       4       4
[redun] | redun_lamin_fasta.finish                          

                0       0       0       0       1       1
[redun] | redun_lamin_fasta.main          

                                  0       0       0       0       1       1
[redun] 
[redun] 
[redun

] Execution duration: 14.24 seconds

View data lineage

artifact = ln.Artifact.get(key="data/results.tgz")
artifact.view_lineage()

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artifact.run.transform.describe()

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Transform: workflow.py (0000)
|   description: CLI: redun
├── uid: CTEut9YSBTZz0000                                     
│   hash: zjZMEeofUMp3FV6fxbgjYg         type: script         
│   branch: main                         space: all           
│   created_at: 2026-10-28 08:23:20 UTC  created_by: testuser1
└── source_code: 
    │ """workflow.py."""
    │ 
    │ # This code is based on a copy from https://github.com/ricomnl/bioinformatics-pi …
    │ # Copyright Rico Meinl 2022
    │ from enum import Enum
    │ 
    │ import lamindb as ln
    │ from redun import File, task
    │ 
    │ import redun_lamin_fasta
    │ from redun_lamin_fasta.lib import (
    │     archive_results_task,
    │     count_amino_acids_task,
    │     digest_protein_task,
    │     get_report_task,
    │     plot_count_task,
    │ )
    │ 
    │ redun_namespace = redun_lamin_fasta.__name__
    │ 
    │ 
    │ class Executor(str, Enum):
    │     default = "default"
    │     process = "process"
    │     batch = "batch"
    │     batch_debug = "batch_debug"
    │ 
    │ 
    │ @task()
    │ def finish(results_archive: File) -> File:
    │ …

artifact.run.describe()

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Run: kmKJaSr (workflow.py)
├── uid: kmKJaSrMZFQTrZ7e                transform: workflow.py (0000)       
│   started_at: 2026-10-28 08:23:20 UTC  finished_at: 2026-10-28 08:23:34 UTC
│   status: completed                                                        
│   branch: main                         space: all                          
│   created_at: 2026-10-28 08:23:20 UTC  created_by: testuser1               
├── cli_args: 
│   │ run workflow.py main --input-dir ./fasta --tag run=test-run
├── report: 6cDeNSb
│   │ → connected lamindb: testuser1/test-redun-lamin
│   │ → created Transform('CTEut9YSBTZz0000', key='workflow.py'), started new Run('kmK …
│   │ • tip: to identify the script across renames, pass the uid: ln.track("CTEut9YSBT …
└── environment: ZZhN6lQ
    │ aiobotocore==3.10.0
    │ aiohappyeyeballs==2.7.1
    │ aiohttp==3.14.5
    │ aioitertools==0.13.0
    │ …

Explore the run on the hub

→ lamin.ai/laminlabs/lamindata/transform/taasWKawCiNA

View the database content

ln.view()

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Artifact

	uid	key	description	suffix	kind	otype	size	hash	n_files	n_observations	...	is_latest	is_locked	created_at	branch_id	created_on_id	space_id	storage_id	run_id	schema_id	created_by_id
id
6	7pMfsmdWDLpLssHt0000	data/results.tgz	None		None	None	94846	2XujeDgKmKAPqNWH3s4VPw	None	None	...	True	False	2026-10-28 08:23:34.258+00:00	1	1	1	1	1.0	None	1
4	GusEh1BzxzeKt2nl0000	fasta/SOX2.fasta	None	.fasta	None	None	414	C5q_yaFXGk4SAEpfdqBwnQ	None	None	...	True	False	2026-10-28 08:23:11.185+00:00	1	1	1	1	NaN	None	1
3	u9ygeSJCACe8CTda0000	fasta/PO5F1.fasta	None	.fasta	None	None	477	-7iJgveFO9ia0wE1bqVu6g	None	None	...	True	False	2026-10-28 08:23:11.185+00:00	1	1	1	1	NaN	None	1
2	A8dVi54KTbWg5SBB0000	fasta/MYC.fasta	None	.fasta	None	None	536	WGbEtzPw-3bQEGcngO_pHQ	None	None	...	True	False	2026-10-28 08:23:11.184+00:00	1	1	1	1	NaN	None	1
1	2xfEH3O2SzsCOmtJ0000	fasta/KLF4.fasta	None	.fasta	None	None	609	LyuoYkWs4SgYcH7P7JLJtA	None	None	...	True	False	2026-10-28 08:23:11.183+00:00	1	1	1	1	NaN	None	1

5 rows × 22 columns

Run

	uid	name	description	entrypoint	started_at	finished_at	params	extra_data	reference	reference_type	...	created_at	branch_id	created_on_id	space_id	transform_id	report_id	environment_id	plan_id	created_by_id	initiated_by_run_id
id
1	kmKJaSrMZFQTrZ7e	None	None	None	2026-10-28 08:23:20.250+00:00	2026-10-28 08:23:34.287322+00:00	None	None	None	None	...	2026-10-28 08:23:20.250+00:00	1	1	1	1	7	5	None	1	None

1 rows × 22 columns

Storage

	uid	root	description	type	region	instance_uid	is_locked	created_at	branch_id	created_on_id	space_id	created_by_id	run_id
id
1	J4W1XaD8b6bR	/home/runner/work/redun-lamin/redun-lamin/docs...	None	local	None	iQlBPgD8uaqR	False	2026-10-28 08:23:08.622+00:00	1	1	1	1	None

Transform

	uid	key	description	kind	source_code	hash	reference	reference_type	version_tag	is_latest	is_locked	created_at	branch_id	created_on_id	space_id	environment_id	plan_id	run_id	created_by_id
id
1	CTEut9YSBTZz0000	workflow.py	CLI: redun	script	"""workflow.py."""\n\n# This code is based on ...	zjZMEeofUMp3FV6fxbgjYg	None	None	None	True	False	2026-10-28 08:23:20.245+00:00	1	1	1	None	None	None	1

Appendix

Map the redun execution id

Export the run information from redun:

redun log --exec --exec-tag run=test-run --format json --no-pager > redun_exec.json

Map it on the run reference:

# load the redun execution id from the JSON and store it in the LaminDB run record
with open("redun_exec.json") as file:
    redun_exec = json.loads(file.readline())
artifact.run.reference = redun_exec["id"]
artifact.run.reference_type = "redun_id"
artifact.run.save()

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Run(uid='kmKJaSrMZFQTrZ7e', name=None, description=None, entrypoint=None, started_at=2026-10-28 08:23:20 UTC, finished_at=2026-10-28 08:23:34 UTC, params=None, extra_data=None, reference='01592df4-0f2f-450f-b6e5-9f4f0b0ebeb1', reference_type='redun_id', cli_args='run workflow.py main --input-dir ./fasta --tag run=test-run', branch_id=1, created_on_id=1, space_id=1, transform_id=1, report_id=7, environment_id=5, plan_id=None, created_by_id=1, initiated_by_run_id=None, created_at=2026-10-28 08:23:20 UTC, is_locked=False)

Map the redun run report

While lamindb auto-tracks the logs of the main python process you might also want to link the dedicated redun logs:

report = ln.Artifact(
    "run_logs.txt",
    description=f"Redun run report of {redun_exec['id']}",
    run=False,
    kind="__lamindb_run__",  # mark as auxiliary artifact for the run
).save()
artifact.run.report = report
artifact.run.save()

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Run(uid='kmKJaSrMZFQTrZ7e', name=None, description=None, entrypoint=None, started_at=2026-10-28 08:23:20 UTC, finished_at=2026-10-28 08:23:34 UTC, params=None, extra_data=None, reference='01592df4-0f2f-450f-b6e5-9f4f0b0ebeb1', reference_type='redun_id', cli_args='run workflow.py main --input-dir ./fasta --tag run=test-run', branch_id=1, created_on_id=1, space_id=1, transform_id=1, report_id=8, environment_id=5, plan_id=None, created_by_id=1, initiated_by_run_id=None, created_at=2026-10-28 08:23:20 UTC, is_locked=False)