-
Notifications
You must be signed in to change notification settings - Fork 354
WIP : Fix strict syntax errors in configs repo (meta PR) #1019
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Open
maxulysse
wants to merge
82
commits into
master
Choose a base branch
from
fix_linting
base: master
Could not load branches
Branch not found: {{ refName }}
Loading
Could not load tags
Nothing to show
Loading
Are you sure you want to change the base?
Some commits from the old base branch may be removed from the timeline,
and old review comments may become outdated.
Open
Changes from 59 commits
Commits
Show all changes
82 commits
Select commit
Hold shift + click to select a range
f70c88c
make vsc_kul_hasselt strict syntax compatible
nvnieuwk cf61456
make pipeline configs strict syntax compatible
nvnieuwk df929f5
fix Alliance_canada
maxulysse 0dfa7f2
fix BI
maxulysse 620bcab
fix bigpurple
maxulysse 6274be5
fix bih
maxulysse e8ad0ca
{USER} -> {System.getenv('USER')}
maxulysse 4c98886
USER -> {System.getenv('USER')}
maxulysse 2862ea4
fix bluebear
maxulysse 946aa69
fix cannon
maxulysse 75417a0
HOME -> {System.getenv('HOME')}
maxulysse e4d2a46
fix ceres
maxulysse de82424
fix cfc
maxulysse 0003b5d
fix cfc_dev
maxulysse 358f1e4
fix cheaha
maxulysse 0dc0198
fix embl_hd
maxulysse b32c1ba
fix fub_curta
maxulysse bdf9e39
fix cheaha
maxulysse 447ffb2
Merge branch 'master' into strict/pipeline-configs
jfy133 ee8b78a
Merge branch 'master' into strict/vsc_kul_hasselt
jfy133 9f06b1e
use ext variables to hold the queue functions
nvnieuwk 2259465
Merge branch 'strict/vsc_kul_hasselt' of github.com:nvnieuwk/configs …
nvnieuwk 94c373a
Merge branch 'master' into fix_linting
maxulysse abf6583
Apply suggestion from @maxulysse
maxulysse adb66eb
Apply suggestion from @maxulysse
maxulysse 333ce0c
bi
maxulysse c5d2674
configtest.nf
maxulysse 834d13e
ucl_myriad
maxulysse 648c20d
incliva
maxulysse 36319d2
pre-commit
maxulysse fd41955
janelia
maxulysse 56d78a2
maestro
maxulysse 4f11282
nfi_gabi
maxulysse 94759f3
sage
maxulysse d41d38d
seadragon
maxulysse bbbb381
software_license
maxulysse b60c7e7
utd_ganymede
maxulysse 2927bd1
wustl_htcf
maxulysse 20bc0c2
nci_gadi
maxulysse d428e00
icr_davros
maxulysse 81e8e2e
crg
maxulysse b44fac1
crg
maxulysse b75aa58
pre-commit
maxulysse f25ceba
utd_juno
maxulysse 612c17b
utd_juno
maxulysse ba59eb7
Merge branch 'master' into strict/pipeline-configs
maxulysse af10567
Merge branch 'strict/pipeline-configs' into fix_linting
maxulysse a8adce2
iris.config
maxulysse 7bd7451
iris.config
maxulysse bae4878
no trace files
maxulysse 68ee06d
Merge branch 'master' into strict/vsc_kul_hasselt
maxulysse 22a7a64
Merge branch 'strict/vsc_calcua' into fix_linting
maxulysse 8e9da3a
Merge branch 'strict/vsc_kul_hasselt' into fix_linting
maxulysse fa35b24
pre-commit
maxulysse 7854267
kaust
maxulysse d14c5f5
kaust
maxulysse 01d63e9
update GHA
maxulysse c1cac76
update GHA
maxulysse 35d0816
update GHA
maxulysse 37aaf3a
Merge branch 'master' into fix_linting
maxulysse d421c00
Merge branch 'master' into fix_linting
maxulysse 8de6d84
pre-commit
maxulysse 8a8bc01
Apply suggestions from code review
maxulysse d8b774c
Apply suggestion from @maxulysse
maxulysse 8f2f955
Merge branch 'master' into fix_linting
maxulysse 9314cd0
improve params
maxulysse 84d73a1
Merge branch 'master' into fix_linting
maxulysse e2e261a
Merge branch 'master' into fix_linting
maxulysse 6b38c8d
Merge branch 'master' into fix_linting
maxulysse c4822ec
Merge branch 'master' into fix_linting
maxulysse 81627bd
alliance_canada
maxulysse ced9c4c
Merge branch 'master' into fix_linting
maxulysse a74749e
Merge branch 'master' into fix_linting
maxulysse 80da799
Merge branch 'master' into fix_linting
maxulysse e559172
restore
maxulysse b24722e
Merge branch 'master' into fix_linting
maxulysse 5983126
Merge branch 'master' into fix_linting
maxulysse d9d1c5e
Merge branch 'master' into fix_linting
maxulysse 4930d6f
Merge branch 'master' into fix_linting
maxulysse eb02ea9
Merge branch 'master' into fix_linting
maxulysse 581b7ff
Merge branch 'master' into fix_linting
maxulysse 386b38c
Merge branch 'master' into fix_linting
maxulysse File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| // Used by https://github.com/nf-core/configs/blob/master/conf/aliance_canada.config | ||
| // Updates settings for Narval | ||
|
|
||
| params.config_profile_description = 'Alliance Canada (Narval) cluster profile provided by nf-core/configs.' | ||
| params.max_memory = 249.GB | ||
| params.max_cpus = 64 | ||
| process { | ||
| resourceLimits = [ | ||
| memory: 249.GB, | ||
| cpus: 64, | ||
| time: 168.h | ||
| ] | ||
| } |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| // Used by https://github.com/nf-core/configs/blob/master/conf/aliance_canada.config | ||
| // Updates settings for Nibi | ||
|
|
||
| params.config_profile_description = 'Alliance Canada (Nibi) cluster profile provided by nf-core/configs.' | ||
| params.max_memory = 750.GB | ||
| params.max_cpus = 192 | ||
| process { | ||
| resourceLimits = [ | ||
| memory: 750.GB, | ||
| cpus: 192, | ||
| time: 168.h | ||
| ] | ||
| } |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| // Used by https://github.com/nf-core/configs/blob/master/conf/aliance_canada.config | ||
| // Updates settings for Rorqual | ||
|
|
||
| params.config_profile_description = 'Alliance Canada (Rorqual) cluster profile provided by nf-core/configs.' | ||
| params.max_memory = 750.GB | ||
| params.max_cpus = 192 | ||
| process { | ||
| resourceLimits = [ | ||
| memory: 750.GB, | ||
| cpus: 192, | ||
| time: 168.h | ||
| ] | ||
| } |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| // Used by https://github.com/nf-core/configs/blob/master/conf/aliance_canada.config | ||
| // Updates settings for Trillium | ||
|
|
||
| params.config_profile_description = 'Alliance Canada (Trillium) cluster profile provided by nf-core/configs.' | ||
| params.max_memory = null | ||
| params.max_cpus = null | ||
| process { | ||
| clusterOptions = "--account=${System.getenv('SLURM_ACCOUNT')} --nodes=1" | ||
| resourceLimits = [ | ||
| time: 168.h | ||
| ] | ||
| } | ||
| executor { | ||
| queueSize = 500 | ||
| } |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Uh oh!
There was an error while loading. Please reload this page.