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Merge dev third rev #20

Merged
merged 630 commits into from
Dec 4, 2024
Merged

Merge dev third rev #20

merged 630 commits into from
Dec 4, 2024

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jvfe
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@jvfe jvfe commented Dec 4, 2024

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

mashehu and others added 30 commits October 16, 2024 11:13
@mashehu
write only relevant fields in .nf-core.yml
6ddd824
@mashehu
switch from docstrings to Field descsriptions
313a4d1
@nf-core-bot
[automated] Update CHANGELOG.md
16e6ff2
@mashehu
Merge pull request nf-core#3225 from nf-core/maxulysse-patch-7
4225001 
Template: Do not assume pipeline name is url
@mashehu
update test to new error
87ab7ee
@mashehu
Merge branch 'fix-pydantic-dump' of github.com:mashehu/tools into fix…
612570f 
…-pydantic-dump
@mashehu
second attempt to add ro crates
6645e4c
@mashehu
fix import
553135a
@mashehu
first running version
bf30f0d
@mashehu
restructure code and add tests
9ed053a
@mashehu
add missing dep
56a170c
@mashehu
add recommendations from comments
8419e9f
@mashehu
add git contributors
bdbc045
@mashehu
fix filename for CI
3ba54c4
@mashehu
better help hint message
9a66883
@mashehu
fix class name
a656617
@mashehu
add correct parent directory to faked crate
fb0d091
@mashehu
add empty ro-crate after sync
2469697
@mashehu
fix tests
f521fa3
@mashehu
fix ci test
797fefb
@mashehu
use github to guess author name, set names as ids if no orcid
9d5251f
@mashehu
add bioschemas, datecreated and datemodified (only set to current tim…
a605ae6 
…e atm)
@mashehu
follow ComputationalWorkflow schema for main entitty.
6c6b8c9
@mashehu
fix date created field
c2f837c
@mashehu
add "about" field to workflow diagram
0778b2a
@mashehu
add input as separate entity
ccfd6d9
@mashehu
add version to main entity
776c6cc
@mashehu
fix incorrect type
a50f12f
@mashehu
switch to add_workflow method to add main entity and add components a…
49592cb 
…s datasets with descriptions
@mashehu
ro_crate -> rocrate
c1d08d7
mirpedrol and others added 25 commits December 2, 2024 10:51
@mirpedrol
update modules and subworkflows
acb9103
@nf-core-bot
[automated] Update CHANGELOG.md
8800b71
@mirpedrol
Merge branch 'dev' into template-monochrome-logs
86a0daa
@mirpedrol
also add monochrome_logs if nf-schema is used
22ff44b
@mashehu
Merge branch 'dev' into seqera_containers_patch2
ed04e1f
@mirpedrol
Merge pull request nf-core#3310 from mirpedrol/template-monochrome-logs
dabf1ef 
Use params.monochrome_logs in the template and update nf-core components
@mashehu
Merge branch 'dev' of github.com:nf-core/tools into fix-yml-config-type
c63f3be 
# Conflicts:
#	CHANGELOG.md
#	nf_core/pipelines/create/create.py
@mirpedrol
add manifest.contributors to nextflow.config
b91bd77
@nf-core-bot
[automated] Update CHANGELOG.md
da021fe
@mirpedrol
fix contributors map
9c8d50f
@LouisLeNezet @ewels
Update nf_core/pipeline-template/.github/CONTRIBUTING.md
df3d25d 
Co-authored-by: Phil Ewels <[email protected]>
@LouisLeNezet
Merge branch 'dev' into documentation
a683b97
@MatthiasZepper @mashehu
Typo in error message.
d72667c 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@MatthiasZepper
Merge pull request nf-core#3293 from MatthiasZepper/seqera_containers…
3c17e81 
…_patch2

Download: Seqera containers Patch 2
@mashehu
test also the main sync function itsel
86b926b
@mashehu
combine json parsing code
ee86c15
@mirpedrol
loop over list of authors to supply contributors
538893c
@mashehu
remove broken test
10e691b
@mashehu
fix type error
11f7f42
@mirpedrol
Merge pull request nf-core#3311 from mirpedrol/manifest_contributors
be5f2e2 
Template: Add `manifest.contributors` to `nextflow.config`
@mashehu
Merge branch 'dev' into documentation
ac5497a
@mashehu
Merge pull request nf-core#3302 from LouisLeNezet/documentation
9d3d074 
Improve documentation writing
@mashehu @mirpedrol
Apply suggestions from code review
eed0598 
Co-authored-by: Júlia Mir Pedrol <[email protected]>
@mashehu
Merge pull request nf-core#3228 from mashehu/fix-yml-config-type
a7351a2 
allow mixed str and dict in lint config
@jvfe
Merge branch 'dev' into merge-dev-third-rev
9c9c66a 
* dev: (458 commits)
  Apply suggestions from code review
  fix type error
  remove broken test
  loop over list of authors to supply contributors
  combine json parsing code
  test also the main sync function itsel
  Typo in error message.
  Update nf_core/pipeline-template/.github/CONTRIBUTING.md
  fix contributors map
  [automated] Update CHANGELOG.md
  add manifest.contributors to nextflow.config
  also add monochrome_logs if nf-schema is used
  [automated] Update CHANGELOG.md
  update modules and subworkflows
  Update gitpod/workspace-base Docker digest to 12853f7 (nf-core#3309)
  Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.1
  Update dawidd6/action-download-artifact action to v7 (nf-core#3306)
  Changelog.
  Include oras:// regex in download to recognize the paths.
  Add dedicated ORAS image format error.
  ...
@jvfe jvfe merged commit c0b51d7 into fix/1927 Dec 4, 2024
58 of 86 checks passed
@jvfe jvfe deleted the merge-dev-third-rev branch December 4, 2024 18:01
@muffato muffato added the bug Something isn't working label Dec 16, 2024
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nf-core module & sub-workflow sharing across organizations
Status: Done
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Enable subworkflows with cross-organi...
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