Configbuilder: nf-core configs create - #3949

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mirpedrol wants to merge 149 commits into

devfrom

Commits on May 25, 2024

Add basic skeleton with welcome screen
jfy133
committed
e93b45a
Update changelgo
jfy133
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266a163
Fix linting failure
jfy133
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71a1475
Linting
jfy133
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a583018

Commits on May 26, 2024

Commits on Jun 1, 2024

Merge branch 'dev' into configbuilder2
jfy133
authored
e8233f5
Fix function calling due to move to generic location
jfy133
committed
17971e6
Copy over @mirpedrol 's writing functions
jfy133
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15f5be8

Commits on Jun 2, 2024

Start making config writing function actually write nextflow configs
jfy133
committed
4af6e99

Commits on Jun 8, 2024

Add URL saving, start adding validation: problem unless everything filled in 'NoneType + str' error
jfy133
committed
2d7863a

Commits on Jun 30, 2024

Commits on Mar 31, 2025

Merge branch 'dev' of https://github.com/nf-core/tools into configbuilder2
mirpedrol
committed
f8ad151

Commits on Apr 2, 2025

Commits on May 5, 2025

Commits on Sep 5, 2025

Commits on Dec 1, 2025

Merge branch 'dev' into configbuilder2
mirpedrol
authored
45aa6fb
Merge pull request #3001 from jfy133/configbuilder2
mirpedrol
authored
908d9fb

Commits on Dec 10, 2025

add default process resource screen and field validation
mgeaghan
committed
b38506f

Commits on Dec 18, 2025

fix field validation and config creation
mgeaghan
committed
e4dbdfb

Commits on Jan 6, 2026

WIP: add custom process config screen
mgeaghan
committed
d1f1cc8

Commits on Jan 7, 2026

WIP: continue work on custom process resource screen
mgeaghan
committed
753ac5e

Commits on Jan 8, 2026

add nonempty validation to process name
mgeaghan
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d15b530
allow reverting from final screen
mgeaghan
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d6d6e11
write basic process config to file
mgeaghan
committed
3ab1999

Commits on Jan 14, 2026

Commits on Jan 20, 2026

add separate screens for process names and labels, switches to determine what to configure
mgeaghan
committed
9f43931

Commits on Jan 28, 2026

use pathlib, clean up time resource string, use snakecase for screen ids
mgeaghan
committed
655d90e

Commits on Jan 29, 2026

refactor process config page into single screen with multiple, removable config widgets
mgeaghan
committed
e7deba0

Commits on Feb 2, 2026

Merge pull request #3974 from mgeaghan/configbuilder
mgeaghan
authored
b6a448e

Commits on Feb 13, 2026

add hpc question to pipeline config branch
mgeaghan
committed
e6c6690

Commits on Feb 18, 2026

Commits on Feb 19, 2026

WIP: working on exporting infra config to file
mgeaghan
committed
e00acf9

Commits on Mar 11, 2026

BUG: GitHub username accepts caps, improve ^@ msg
fredjaya
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36d7aed
MAINT: remove duplicate field_validator
fredjaya
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8df673a
MAINT: Tidy git handle validation
fredjaya
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aac51fe
MAINT: infra retries validated
fredjaya
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8fb1d27
MAINT: ui typo
fredjaya
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e38d512
MAINT: validate paths and uris
fredjaya
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277a8ef
add igenomes, scratch, retires to final config file, update autofill of container cache dir
mgeaghan
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17d4bac
Merge remote-tracking branch 'upstream/configbuilder' into configbuilder
fredjaya
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2f7d538
BUG: Fix bad merge zzz
fredjaya
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9b0dad6
MAINT: Move containers to imported variable
fredjaya
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0578de6
MAINT: Update pydantic model
fredjaya
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bba6c10
WIP: Add unvalidated model
fredjaya
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f543644
add container scope
mgeaghan
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a5a3229
feat(hpc): added methods to obtain default queues in hpc
nbtm-sh
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a2708f1

Commits on Mar 12, 2026

fix(pbs): fix pbs list command when getting config
nbtm-sh
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f01d1ef
fix(pbs): fix split
nbtm-sh
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0a84ba0
feat(queue): autofill default queue if available
nbtm-sh
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4b1d628
WIP: I have made a mess
fredjaya
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377de87
MAINT: Max resourcelimits as required fields
fredjaya
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79da1cb
fix(pbs): fix broken pbs queue listing
nbtm-sh
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ad9d33c
DEV: Placeholder validator
fredjaya
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0ee7a1c
Merge branch 'configbuilder' of https://github.com/nf-core/tools into configbuilder
fredjaya
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4708dbf
fix(slurm): fix listing slurm queues
nbtm-sh
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40ef725
Merge pull request #4101 from fredjaya/configbuilder
mgeaghan
authored
ccb7f3f
Merge pull request #4105 from nf-core/add-get-default-queue
mgeaghan
authored
59daade
feat(serial): add serial file
nbtm-sh
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9896d1b
Merge branch 'configbuilder' into fix-configbuilder-queue-suggestions
mgeaghan
authored
ae8f7eb
Merge pull request #4108 from nf-core/fix-configbuilder-queue-suggestions
mgeaghan
authored
f28e0b4
feat(serial): add oneliner option
nbtm-sh
committed
6cf6cbb
add executor scope and additional executor fields, e.g. poll interval and queu size
mgeaghan
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ec7a42a
feat(serial): add serial method to configuration file
nbtm-sh
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c571344
bugfix: remove erroneous double up of 'memory' setting
mgeaghan
committed
9b2feb6
feat(config): replace output methods wiht serial methods
nbtm-sh
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131fb35
fix(util): rename serial to serial_hpc
nbtm-sh
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de40267
Merge branch 'configbuilder' into add-nextflow-serial
nbtm-sh
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7b76135

Commits on Mar 13, 2026

validate new infrastructure fields
mgeaghan
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c25d25f
feat(serial): add option to remove quotes around strings for one-liners
nbtm-sh
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9bd081e
feat(serial): set default values for dumps
nbtm-sh
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0f25c5d
feat(serial): remove quotes around list dicts
nbtm-sh
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b9f57af
fix(serial): output formatted resource information
nbtm-sh
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e1041cc
feat(serial): add base pipeline seiral method
nbtm-sh
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b00f350
this with
amarinderthind
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2e00825
Added drop down option for a field
amarinderthind
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ad262ae
feat(utils): add methods
nbtm-sh
committed
1d1fc9e
validate custom process queue
mgeaghan
committed
85403af
revert(create): revert method call to serial()
nbtm-sh
committed
e96c8dc
updated pbs to pbspro
amarinderthind
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892025d
feat(config): change general_config_type to a boolean value
nbtm-sh
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cb1cfff
feat(is_infra): set to true for hpc configuration
nbtm-sh
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c7deeca
feat(is_infra): set to true for infra config
nbtm-sh
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5c92761
revert(infra): remove infra from pipeline config
nbtm-sh
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f354b33
feat(infra): add infrastructure variable to basic details
nbtm-sh
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6fe0907
revert(infra): remove infrastructure option from hpc config
nbtm-sh
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290a2fe
fix(utils): remove trailing whitespace
nbtm-sh
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a22e0ef
Merge pull request #4118 from nf-core/fix-general-config-type
mgeaghan
authored
0ff342f
Merge branch 'configbuilder' into add-nextflow-serial
nbtm-sh
committed
7f1b7c3
Merge pull request #4115 from amarinderthind/configbuilder
mgeaghan
authored
e044195
feat(serial): add withName and withLabel to config
nbtm-sh
committed
98d78b9
fix(serial): change labelled
nbtm-sh
committed
7bb3ad0
fix(config): fix error when creating withLabel entries
nbtm-sh
committed
a602113

Commits on Mar 23, 2026

Commits on Mar 24, 2026

handle unset custom resources
mgeaghan
committed
2cc93cc
Merge branch 'dev' into configbuilder
mgeaghan
authored
86657e0
fix linting errors
mgeaghan
committed
2939e91

Commits on Mar 25, 2026

fix more linting issues
mgeaghan
committed
e9d8d82
WIP - add config builder app tests
mgeaghan
committed
3db70bc

Commits on Mar 27, 2026

exclude snapshots from precommit linting
mgeaghan
committed
79ade5e
WIP update configbuilder app infra tests
mgeaghan
committed
a678c98

Commits on Mar 29, 2026

fix test linting, fix typo in finalinfradetails
mgeaghan
committed
f290340
Merge remote-tracking branch 'origin/dev' into configbuilder
mgeaghan
committed
c092aa7
update final infra detail test snapshots
mgeaghan
committed
12d4da7

Commits on Apr 21, 2026

WIP: implementing feedback
mgeaghan
committed
e8f1f9d

Commits on Apr 22, 2026

WIP: implementing more feedback, adding cache dir memory to final infra details
mgeaghan
committed
56c1d81

Commits on May 8, 2026

WIP: implementing more feedback, finished setting default process resources
mgeaghan
committed
8ec71d9

Commits on May 11, 2026

WIP: implementing more feedback
mgeaghan
committed
17bda0a

Commits on May 12, 2026

Fix validation for nf core pipeline configs
mgeaghan
committed
803b66c

Commits on May 13, 2026

WIP: continue adding tui tests
mgeaghan
committed
5eb11ef

Commits on May 18, 2026

finish adding tui tests, test writing configs
mgeaghan
committed
0420d1d
Update TUI test snapshots
mgeaghan
committed
d834f42

Commits on May 19, 2026

Commits on May 20, 2026

WIP: more unit tests for validation code
mgeaghan
committed
aa3b24f

Commits on May 22, 2026

merge latest dev changes
mgeaghan
committed
a083abd
finish validation unit tests
mgeaghan
committed
75b480c
finish unit tests, reformat, fix failing app tests
mgeaghan
committed
9a0c699
reformat again and fix ruff check errors
mgeaghan
committed
967ae26
resize infra final details screen in test
mgeaghan
committed
200d862
update snapshots
mgeaghan
committed
fb8d65a

Commits on Jul 9, 2026

remove empty config sections, clean up resource request formatting
mgeaghan
committed
3393082
[automated] Fix code linting
nf-core-bot
committed
d67ba05

Commits on Jul 10, 2026

update wording, WIP updating optional/required field markers in finalinfradetails
mgeaghan
committed
b7d2742

Commits on Jul 13, 2026

fix typos, improve explanatory text, make cachedir dynamic
mgeaghan
committed
e810969

Commits on Jul 22, 2026

add more allowed schedulers: moab, nqsii, lsf
mgeaghan
committed
c696c88

Commits on Jul 27, 2026

WIP: hiding queue fields when not supported
mgeaghan
committed
78ffba2

Commits on Jul 30, 2026

add support for htcondor, hyperqueue, flux, tcs
mgeaghan
committed
5791edb