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Syncing
xxxxxxxxxx
2025-06-27
Agenda
Minutes
2025-05-30
Agenda
pipeline/main.nf
file for workflows instead ofpipeline.nf
Minutes
Action Items
2025-04-25
Agenda
test_full
profiles for all nf-core pipelines. Many orgs run these pipelines with full test profiles regularly for infrastructure tests etc. Default resource configurations are unnecessarily wasteful in most cases! I did some work to generate optimised configs for all pipelines that had succesfull runs since beginning 2024 here : https://github.com/FloWuenne/megatest-resource-optimization/tree/main/optimized_configsMinutes
maintainer
tag of contribtuion in nextflow.config manifest?test_full
latest-everything
issue (likely next week ™️)Action Items
2025-02-28
Attendance
Agenda (Don't edit, only append!)
Minutes
Action Points
2025-01-31
Attendance
Agenda (Don't edit, only append!)
Minutes
Action Points
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Learn More →2024-11-29
Attendance
Agenda (Don't edit, only append!)
workflowCitation()
function completely? or add it back to the pipelines template? https://github.com/nf-core/modules/pull/7094 (Júlia)nf-test.yml
: Runs Nextflow tests for workflows and modules across profiles using matrixed shards.gpu-tests.yml
: Executes GPU-specific Nextflow tests for changes in GPU-related workflows and modules.nf-test-action.yml
: Provides a reusable action to standardize and run Nextflow tests with configurable setups.detect-nf-test-changes
: Include tags / Exclude tagsMinutes
TANGENT: automation of releases?
workflowCitation()
James wants Maxime to stop experimenting on Sarek and rnaseqSateesh and Edmund exprimenting on modules ;)Action Points
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Learn More →2024-10-25
Attendance
Agenda (Don't edit, only append!)
Action points from last time
Sign up for re-booted helpdesk: https://docs.google.com/spreadsheets/d/1c1Pz97W5azlPph9iiORAxRCLc6q4KBQRfK4M0h127KM/edit?usp=sharing
nf-core hackathon!
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Learn More →Mahesh Binzer-PanchalMahesh PoC of nf-test config clean up: https://github.com/nf-core/modules/pull/6788
Mahesh Binzer-PanchalWhat to do about module maintainers holding up contributions? https://github.com/nf-core/modules/pull/5706
(sateesh) Discuss the depreciation of
conf/modules.config
in favor of individual configs. Example implementation - methylseq dev[@jfy133] despite assumed knowlege,multiMap
indeed does not ensure syncronised subchannels - as listed in updated docs under the new note block. We should change modules specs to have a single tuple to enure all files come intogether syncronisedWe shouldn't mass change all modules, just update over timeMatthias De Smet Module guidelines points 3.3 and 3.6 seem to contradict each other. We should remove the ambiguous language and define whether or not each output file type MUST have their own output channel
Mahesh Binzer-Panchal Monthly update of changes in guidelines or PR reviewing. It's quite easy to fall behind and it would be nice to have monthly coverage of what's changed and go over how to review a PR. This could be a part of the office hours.
Minutes
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Learn More →modules.conf
into one per modulemodules.conf
)nextflow.config
)nextflow config
should properly print out stuff, then it's OK (a user can use that to view)Action points
2024-09-27
Agenda
2024-08-30
Attendance
Agenda (Don't edit, only append!)
2024-07-28
Attendance
Agenda (Don't edit, only append!)
Minutes
Last meeting action points:
dev
version of modules guidelines?Action points
2024-06-28
Attendance
Agenda
Actions from last time:
Jon's subworkflows name proposal:
PREPARE_RNASEQ_READS_FOR_ALIGNMENT
FASTQ_TRIM_QC_SUBSAMPLE_FASTQC_UMITOOLS_TRIMGALORE_SUBSAMPLE_FQ_SALMON_SORTMERNA
MY_SUBWORKFLOW_FINAL_FINAL_3_FINAL
FASTQ_QC_TRIM_FILTER_REMOVE_STRANDEDNESS
FASTQ_PREPROCESS_FOR_RNASEQ
FASTQ_PREPROCESS_RNASEQ
PREPROCESS_RNASEQ
PREPARE_RNASEQ_READS_FOR_ALIGNMENT
Do we give Maxime his own pipeline (an extra one since he already has many toys)?
Discuss problems with test-datasets
How can we ensure the full size tests are run before a release?
Do we need more frequent/longer meetings, or sub-group meetings (e.g. modules/subworkflows)
Minutes
PREPARE_RNASEQ_READS_FOR_ALIGNMENT
FASTQ_TRIM_QC_SUBSAMPLE_FASTQC_UMITOOLS_TRIMGALORE_SUBSAMPLE_FQ_SALMON_SORTMERNA
MY_SUBWORKFLOW_FINAL_FINAL_3_FINAL
FASTQ_QC_TRIM_FILTER_REMOVE_STRANDEDNESS
(input, generic process description)FASTQ_PREPROCESS_FOR_RNASEQ
FASTQ_PREPROCESS_RNASEQ
PREPROCESS_RNASEQ
PREPARE_RNASEQ_READS_FOR_ALIGNMENT
- Lots of customers people want this at Seqera, as do in other places
- Should push forward
- Where does documentation then go (if you start merging pipelines together, can default merge them)
- Nextflow code should be relatively easy, but it's everything around it that is the issue
- Working group?
- Turn down for now, because e.g. docs maintaince burden is too high; as it's still an early PoC -> Still too many questions about what is a subworkflow/workflow
Action Points
2024-05-31
Attendance
Agenda
meta.yml
(https://github.com/nf-core/modules/issues/4983 and https://github.com/nf-core/tools/pull/2789)Minutes
preprocess
is bad, but rather e.g. trim, removerna, -> semantics in names is badActions
2024-04-26
Attendance
Agenda
Minutes
Action points
2024-03-29
2024-02-23
Attendence
Agenda
- Blog preview
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Learn More →- Want to build capacity by creating opportunities to upskill
- Aims to complement Slack
- It's a pilot, we want feedback!
- Time needs to be decided
- Action: @ChrisHakk to organise a poll in maintainers channel to find "best" time.
- Aim to kick off after the hackathon so be can benifit from paid Gather space.
ch_
prefix for channels.Actions points from last meeting:
2024-01-26
Attendence
@jfy133, @maxulysse, @kOcBx-beQZW6WOsI5UVQcA, Ram, @emiller, @YO3oG0hdSw2Gv5IWHc0nfA, Jasmin, Jon, Jonas, @JoseEspinosa, @jmir, @mashehu, Nicolas, Simon, Sofia,
Agenda
meta2
->meta_file
?: https://github.com/nf-core/modules/pull/4594- The image file may be corrupted
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Learn More →- The image file may be corrupted
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Learn More →- The image file may be corrupted
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Learn More →- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
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Learn More →- The image file may be corrupted
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Learn More →Action Points
2023-12-15 - Cancelled
Agenda
2023-11-24
Agenda
check_samplesheet.py
NXF_SINGULARITY_HOME_MOUNT
in the template config?Actions point
2023-10-27
Who
Focus is hackathon follow up: nf-test migration and refactoring pipelines.
@mashehu is leading the infrastructure front
@maxulysse is leading the pipeline refactoring front
@nvnieuwk and Jonathan Manning will be coordinating and managing the general effort and making sure we stay on target.
2023-09-22
When/Where
https://zoom.us/j/93254682925?pwd=TW9GdU1YeU1EVnE2aFMvdDNkY2t1Zz09
Who
Action Points from last time
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Learn More →Agenda
Action Points
2023-06-30
When/Where
Zoom: https://eu01web.zoom.us/j/64977955782?pwd=YzRVRHArcGZ4MkN3NllZT2pRanhYQT09
Who
@jfy133
@jasmezz
@nvnieuwk
@maxulysse
@jmir
@FriederikeHanssen
@JoseEspinosa
@louperelo
@mashehu
and
Rob
Daniel
Sofia
Ram
Matthias D
Sateesh
Edmund
(and whoever else I forgot)
Agenda
https://www.atlassian.com/blog/git/written-unwritten-guide-pull-requests
https://www.freecodecamp.org/news/git-best-practices-commits-and-code-reviews/)
Action Points
Meeting 2023-05-26
When/Where
Gather! (probably or not…)
Zoom: https://eu01web.zoom.us/j/67778335655?pwd=MXQwaGZKT1JMeXFJTWdiWGRpQWVsQT09
Who
@asp8200
@JoseEspinosa
@sateeshperi
@jfy133
@jmir
@ramprasadn
@nvnieuwk
@louperelo
@maxulysse
@pinin4fjords
Agenda
Action Points
nf-core/maintainers meeting
Meeting 2023-04-28
When/Where
2023-4-28 15:00-16:00 CEST, gather.town
Who?
@mashehu , @jfy133 , @louperelo, @ramprasadn, @pinin4fjords, @jmir, @jasmezz, @robsyme, @christopher-mohr
Agenda
Review last meetings TODO
Guidelines
foldernew tools release upcoming
If time: review orphaned questions
nf-test pipeline PRs for review:
fetchngs
rnaseq
methylseq
demultiplex
viralrecon
ampliseq
nascent
viralintegration
Action Points
Meeting 2023-03-31
When/Where
2023-03-31 15:00-16:00 CET , nf-core office gather.town
Who?
Agenda
Meeting was cancelled because everyone was hackathon-tired
Meeting 2023-02-24
When/Where
2023-02-24 15:00-16:00 CET , nf-core office gather.town
Who?
@jfy133 @pinin4fjords @matthdsm @jmir @nvnieuwk, @mashehu, @louperelo, @ChrisHakk, @emiller
Agenda
stub
section be required for new modules? (@matthdsm, @maxulysse)TODO
Issues for:
Review slack channels during spring cleaning
Meeting 2023-01-27
When/Where
2023-01-27 15:00-16:00 CET , nf-core office gather.town
Who?
@maxulysse, James, Jon, Jasmin, Matthias H, Louisa, Moritz, Nicolas, Gisela, Simon, Júlia, @emiller, Matthias dS, Rike, Daniel, Chris, Sofia
TODO (for next time)
Agenda
Review previous meeting TODO
master
✅ Review spring cleaning plan from Chris/James
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Learn More →✅ nf-validate update from Júlia –> meeting notes
Meeting Notes
- Couldn't do it on a single channel which was the main issue (request-reviews), just use markdown instead (or manually close the preview)
TODOs
Meeting 2022-11-25
When?
Friday, 25 November⋅13:00 – 14:00 (CET), nf-core office gather.town
Who?
Rike*, James, @maxulysse, Matthias De Smet, Jon Manning (Healx Ltd, Cambridge), Nicolas, Daniel Straub (@d4straub)*, Moritz Beber, Gisela Gabernet (@ggabernet)*, Chris Mohr, Anders Jemt, Jose Espinosa-Carrasco, Louisa Perelo (@louperelo)*, Ram, Harshil, Simon Pearce, Matthias Hörtenhuber, Anders Sune Pedersen (Danish National Genome Center), Matthieu Muffato (@muffato, Wellcome Sanger Institute)
* Quantitative Biology Center (QBiC), Eberhard Karls Universität Tübingen, Germany
TODOs (for next time):
add name/affiliation here (in no particular order!)
Dormant contributors
Ping Rike if you are not in the right teams (github, slack)
Reserve week of 7th March for spring cleaning week!
master
Agenda
General Topics
ensemblvep
,snpeff
,bclconvert
,bcl2fastq
: @matthdsm + @maxulysse)Google sheet–> Board view is spread sheet like enough- The image file may be corrupted
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Learn More →Spring Cleaning!
Organised by: James & Chris Hakkaart
When:
- week of 07th of March 2023, before the hackathon
- Kick-off meeting on the monday, distribute tasks, form smaller groups
- Spread throughout the week as time permits
- Closing meeting on Friday
Idea:
Lots of old issues, PRs, test data etc. that we need to clean up once a year as maintainers.
What should we do?
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Learn More →Post-hackathon events:
Topics to discuss in the upcoming months
nf-test
Orphaned Qs
If still relevent