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Merged
pditommaso merged 84 commits into from
Mar 17, 2026
Merged

Module system #6650

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59983c1
Add Nextflow Development Constitution
pditommaso Nov 17, 2025
fccfc74
Module adr v1
pditommaso Nov 24, 2025
20020a7
Module adr v2
pditommaso Nov 25, 2025
226d4ee
ADR: Nextflow remote modules system v2.1
pditommaso Dec 11, 2025
513fa6a
Merge master into 251117-module-system [ci skip]
pditommaso Dec 11, 2025
beaaa08
Merge branch 'master' into 251117-module-system
pditommaso Dec 15, 2025
8e681e9
Add detailed CLI command descriptions to module system ADR [ci skip]
pditommaso Dec 15, 2025
c6ca725
Merge branch 'master' into 251117-module-system
pditommaso Jan 6, 2026
5df12cd
Simplify module spec: unify dependencies under requires
pditommaso Jan 6, 2026
01c777a
Add structured tool arguments to module spec schema
pditommaso Jan 6, 2026
7e12f3a
Update adr/20251114-module-system.md [ci skip]
pditommaso Jan 7, 2026
5a01d00
Update adr/20251114-module-system.md [ci skip]
pditommaso Jan 7, 2026
4779d50
Update adr/20251114-module-system.md [ci skip]
pditommaso Jan 7, 2026
5b1d4e5
Update adr/20251114-module-system.md [ci skip]
pditommaso Jan 14, 2026
a06ab7a
Fix inconsistencies in module system ADR [ci skip]
pditommaso Jan 14, 2026
f7dab8d
Fix registry API path in comparison table [ci skip]
pditommaso Jan 14, 2026
0242a4a
Fix checksum format: sha256- -> sha256: [ci skip]
pditommaso Jan 14, 2026
5461f5b
Update module API to match registry implementation [ci skip]
pditommaso Jan 14, 2026
926052c
Update adr [ci skip]
pditommaso Jan 15, 2026
ec187fd
Simplify module storage and verification model [ci skip]
pditommaso Jan 15, 2026
46c6060
Update adr/20251114-module-system.md [ci skip]
pditommaso Jan 15, 2026
1b0ab1a
Clarify module resolution rules for version changes vs local modifica…
pditommaso Jan 15, 2026
7a1e62e
ADR v2.3: Fix resolution rules consistency and add version entry [ci …
pditommaso Jan 15, 2026
c6eaabb
Fix Version 2.1 date typo: 2025 -> 2024 [ci skip]
pditommaso Jan 15, 2026
daf01be
Merge branch 'master' into 251117-module-system [ci skip]
pditommaso Jan 15, 2026
c8bc50d
Add module system client specification [ci skip]
pditommaso Jan 15, 2026
68b202f
Remove transitive dependency resolution from module system [ci skip]
pditommaso Jan 15, 2026
d118d5a
Update adr/20251114-module-system.md [ci skip]
pditommaso Jan 21, 2026
ffe1116
Update adr/20251114-module-system.md [ci skip]
pditommaso Jan 21, 2026
806a41f
Update modules plan [ci skip]
pditommaso Jan 19, 2026
f7e9def
Remove tools config [ci skip]
pditommaso Jan 21, 2026
474eb75
Simplify module system requires definition [ci skip]
pditommaso Jan 22, 2026
5581257
Replace tool arguments with module parameters in ADR [ci skip]
pditommaso Jan 23, 2026
903c740
Update specs + adr [ci skip]
pditommaso Jan 23, 2026
82d90d6
Resolve some conflicts with nextflow-io/schemas#10
bentsherman Jan 25, 2026
d86c211
Update adr/20251114-module-system.md [ci skip]
pditommaso Jan 26, 2026
8fa6478
Extract module parameters to separate spec [ci skip]
pditommaso Jan 28, 2026
3bce3eb
Merge branch 'master' into 251117-module-system
jorgee Feb 10, 2026
6cfa59f
Merge branch 'master' into 251117-module-system
jorgee Feb 25, 2026
1d6005b
docs: clarify path name for staged task inputs (#6869)
LarytheLord Feb 26, 2026
d9952fb
Add devcontainer (#6792)
PeterKneale Feb 26, 2026
481b90f
Fix vertical alignment in timeline report (#6794)
PeterKneale Feb 26, 2026
4ad9e34
Ensure main script is first in the WorkflowRun lineage record (#6845)
jorgee Feb 26, 2026
4d8ef30
Add whitespace rules to .editorconfig (#5606)
ewels Feb 26, 2026
0228a4e
docs: Update your first script to use outputs (#6500)
christopher-hakkaart Feb 26, 2026
a1a046a
Update AWS CLI install docs to bypass conda install TOS prompt (#6685)
rzelle-lallemand Feb 27, 2026
3830af3
Clarify onError and onComplete handler descriptions (#6709) [ci fast]
colinbrislawn Feb 27, 2026
28458b5
Use explicit memory units for LSF executor (#5217)
bentsherman Feb 27, 2026
911d399
Treat LSF job status UNKWN as HOLD (#5756)
bentsherman Feb 27, 2026
d17e6c1
Allow boolean params to implicitly default to false (#6764)
bentsherman Feb 27, 2026
d0a9fbd
Sched core implementation alpha1 (#6242)
pditommaso Feb 27, 2026
153d937
Revert version 26.01.1-edge
pditommaso Feb 27, 2026
5c67090
Bump copyright 2026
pditommaso Feb 27, 2026
b0a1877
Handle Azure Batch ActiveJobAndScheduleQuotaReached with retry (#6874)
adamrtalbot Feb 27, 2026
d8a7fc2
[ci fast] Add agent output mode (NXF_AGENT_MODE)
edmundmiller Feb 28, 2026
f13573d
Bump nf-amazon@3.7.1
pditommaso Feb 28, 2026
837af5f
Bump nf-azure@1.22.0
pditommaso Feb 28, 2026
6b58251
Bump nf-google@1.26.1
pditommaso Feb 28, 2026
daf9f36
Bump nf-tower@1.21.0
pditommaso Feb 28, 2026
3c8752a
Bump nf-seqera@0.12.0
pditommaso Feb 28, 2026
53df43c
Bump nf-tower@1.21.0 nextflowVersion
pditommaso Feb 28, 2026
7a17237
Bump nf-seqera@0.12.0 nextflowVersion and README
pditommaso Feb 28, 2026
d2cd6f0
Fix AgentLogObserver println clash with Groovy GDK method
pditommaso Feb 28, 2026
e79eb98
Add Summary section to plugin README files
pditommaso Feb 28, 2026
15e1eef
[release] [ci fast] Nextflow version 26.02.0-edge
pditommaso Feb 28, 2026
51098d3
Fix docs [ci skip]
pditommaso Mar 2, 2026
9a3c847
Add logStreamId to Tower task record (#6877)
pditommaso Mar 2, 2026
4bf4b75
Don't include container in task trace when containers are not enabled…
bentsherman Mar 2, 2026
3137069
Propagate errors from workflow outputs (#6876)
bentsherman Mar 2, 2026
8644993
Fix type detection of CLI params in v2 config parser (#6765)
bentsherman Mar 2, 2026
7d772ea
Add NVMe disk allocation and diskMountPath support (#6879) [ci fast]
pditommaso Mar 2, 2026
b0feed3
Merge remote-tracking branch 'origin/master' into 251117-module-syste…
jorgee Mar 4, 2026
f145979
Version 2.7: rename `.checksum` to `.module-info`, remove `@` prefix …
bentsherman Mar 10, 2026
583285c
Module System Implementation (#6768)
jorgee Mar 10, 2026
b2fa0f8
minor edits
bentsherman Mar 13, 2026
9b647ef
Cleanup module run output
bentsherman Mar 13, 2026
00824f3
Fix meta.yaml -> meta.yml, module manifest -> module spec
bentsherman Mar 13, 2026
24e14ee
Merge branch 'master' into 251117-module-system
bentsherman Mar 13, 2026
2e183b5
Fix failing test
bentsherman Mar 13, 2026
0a7ef22
fix tests
jorgee Mar 16, 2026
6c15bc8
modify module list to skip subdirectories of directories that already…
jorgee Mar 16, 2026
3be2f02
Update docs
bentsherman Mar 16, 2026
512b27d
Merge branch 'master' into 251117-module-system
bentsherman Mar 16, 2026
34426ea
Apply suggestion from @pditommaso [ci skip]
pditommaso Mar 16, 2026
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