Nextflow#
Nextflow is a workflow management system used for executing scientific workflows across platforms scalably, portably, and reproducibly.
Here, we鈥檒l run a demo of the microscopy pipeline mcmicro to correct uneven illumination. Reference
Note
Typically, you run the Nextflow workflow from the command line or Seqera Platform and then register input and output data with a script. The Seqera Platform allows for post-run scripts that can automate this process.
Let鈥檚 load an instance that already has example data.
!lamin load nextflow-mcmicro
Show code cell output
馃挕 connected lamindb: testuser1/nextflow-mcmicro
import lamindb as ln
馃挕 connected lamindb: testuser1/nextflow-mcmicro
Run and register Nextflow workflow#
!nextflow run https://github.com/labsyspharm/mcmicro --in exemplar-001 --start-at illumination --stop-at registration
Show code cell output
N E X T F L O W ~ version 23.10.1
Launching `https://github.com/labsyspharm/mcmicro` [zen_hawking] DSL2 - revision: 69ee2efe21 [master]
[56/c7cf88] Submitted process > illumination (2)
[76/e8638e] Submitted process > illumination (3)
[51/714ef6] Submitted process > illumination (1)
[f5/b28fb5] Submitted process > registration:ashlar (1)
Now we register our Nextflow run by running our registration script.
!python register_mcmicro_run.py
Show code cell output
馃挕 connected lamindb: testuser1/nextflow-mcmicro
馃挕 saved: Transform(uid='vBg3mujGt2QVvBup', name='mcmicro', version='1.0.0', type='pipeline', reference='https://github.com/labsyspharm/mcmicro', updated_at=2024-05-01 11:10:52 UTC, created_by_id=1)
馃挕 saved: Run(uid='3DSH7zSzFd5S4okTCr99', transform_id=2, created_by_id=1)
Data lineage#
View data lineage:
output = ln.Artifact.filter(description__icontains="mcmicro").one()
output.view_lineage()
View the database content:
ln.view()
Artifact
| uid | storage_id | key | suffix | accessor | description | version | size | hash | hash_type | n_objects | n_observations | transform_id | run_id | visibility | key_is_virtual | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 11 | ULtxc8jLAN7Jo2lu1h2F | 1 | exemplar-001/registration/exemplar-001.ome.tif | .tif | None | mcmicro | None | 175490712 | txf98DOQS30uC-kz_uqK77 | sha1-fl | None | None | 2 | 2 | 1 | False | 2024-05-01 11:10:53.779895+00:00 | 2024-05-01 11:10:53.779932+00:00 | 1 |
| 10 | x2aSzx3rUkbT9uSR6PLg | 1 | exemplar-001/illumination/exemplar-001-cycle-0... | .tif | None | None | None | 22119019 | _PVbSfSL5apmaZkcpL2mbw | md5 | None | None | 1 | 1 | 1 | False | 2024-05-01 11:08:54.852940+00:00 | 2024-05-01 11:08:54.852975+00:00 | 1 |
| 9 | GDtuemHYSbaNFsW97onJ | 1 | exemplar-001/illumination/exemplar-001-cycle-0... | .tif | None | None | None | 22119019 | fUw4NVqV-Zy_OdxiMetlfg | md5 | None | None | 1 | 1 | 1 | False | 2024-05-01 11:08:54.850989+00:00 | 2024-05-01 11:08:54.851010+00:00 | 1 |
| 8 | PUxouEgLn6Zd2nRbPyAS | 1 | exemplar-001/illumination/exemplar-001-cycle-0... | .tif | None | None | None | 22119019 | H_ya8KoVaaeu_Ve_N14TAg | md5 | None | None | 1 | 1 | 1 | False | 2024-05-01 11:08:54.850386+00:00 | 2024-05-01 11:08:54.850406+00:00 | 1 |
| 7 | WpO5a6APWxg9bGK6ucOr | 1 | exemplar-001/illumination/exemplar-001-cycle-0... | .tif | None | None | None | 22119019 | qpmIHKbuxwe2sE_rdcPqfA | md5 | None | None | 1 | 1 | 1 | False | 2024-05-01 11:08:54.849781+00:00 | 2024-05-01 11:08:54.849802+00:00 | 1 |
| 6 | vaQ8rqk2GwGsq5IjKqU9 | 1 | exemplar-001/illumination/exemplar-001-cycle-0... | .tif | None | None | None | 22119019 | idW8uRMTLfXNJHnboZy8GQ | md5 | None | None | 1 | 1 | 1 | False | 2024-05-01 11:08:54.849167+00:00 | 2024-05-01 11:08:54.849188+00:00 | 1 |
| 5 | yuNuQTvndtdnKgfCpMmt | 1 | exemplar-001/illumination/exemplar-001-cycle-0... | .tif | None | None | None | 22119019 | Yw4DJkg2QQ7ez4j2_qWN_Q | md5 | None | None | 1 | 1 | 1 | False | 2024-05-01 11:08:54.848517+00:00 | 2024-05-01 11:08:54.848538+00:00 | 1 |
Run
| uid | transform_id | started_at | finished_at | created_by_id | json | report_id | environment_id | is_consecutive | reference | reference_type | created_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 1 | T1m3JHGkRcC6XrT52eaK | 1 | 2024-05-01 11:08:35.915465+00:00 | None | 1 | None | None | None | True | None | None | 2024-05-01 11:08:35.915620+00:00 |
| 2 | 3DSH7zSzFd5S4okTCr99 | 2 | 2024-05-01 11:10:52.890295+00:00 | None | 1 | None | None | None | None | nextflow\n799960a8-dfcf-4f84-bf53-415ffe457658 | nextflow_id | 2024-05-01 11:10:52.890448+00:00 |
Storage
| uid | root | description | type | region | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|
| id | ||||||||
| 1 | EH936rNQ | /home/runner/work/nextflow-lamin-usecases/next... | None | local | None | 2024-05-01 11:08:34.281568+00:00 | 2024-05-01 11:08:34.281593+00:00 | 1 |
Transform
| uid | name | key | version | description | type | latest_report_id | source_code_id | reference | reference_type | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 2 | vBg3mujGt2QVvBup | mcmicro | None | 1.0.0 | None | pipeline | None | None | https://github.com/labsyspharm/mcmicro | None | 2024-05-01 11:10:52.886700+00:00 | 2024-05-01 11:10:52.886733+00:00 | 1 |
| 1 | XBFQnGeFoIIFirxP | Download | None | None | None | pipeline | None | None | None | None | 2024-05-01 11:08:35.910323+00:00 | 2024-05-01 11:08:35.910360+00:00 | 1 |
User
| uid | handle | name | created_at | updated_at | |
|---|---|---|---|---|---|
| id | |||||
| 1 | DzTjkKse | testuser1 | Test User1 | 2024-05-01 11:08:34.277453+00:00 | 2024-05-01 11:08:34.277483+00:00 |
Clean up the test instance:
!lamin delete --force nextflow-mcmicro
Show code cell output
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.10.14/x64/bin/lamin", line 8, in <module>
sys.exit(main())
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/rich_click/rich_command.py", line 360, in __call__
return super().__call__(*args, **kwargs)
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/rich_click/rich_command.py", line 152, in main
rv = self.invoke(ctx)
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/lamin_cli/__main__.py", line 103, in delete
return delete(instance, force=force)
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/lamindb_setup/_delete.py", line 130, in delete
n_objects = check_storage_is_empty(
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/lamindb_setup/core/upath.py", line 720, in check_storage_is_empty
raise InstanceNotEmpty(message)
lamindb_setup.core.upath.InstanceNotEmpty: Storage location contains 145 objects (2 ignored) - delete them prior to deleting the instance
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