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DO NOT MERGE! A brave new world #115

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wants to merge 440 commits into from
Closed

DO NOT MERGE! A brave new world #115

wants to merge 440 commits into from

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subwaystation
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
    • If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
    • If necessary, also make a PR on the nf-core/pangenome branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

Opening this up for @ggabernet. I think this is the better way for you to understand the actual changes.

@subwaystation
smoothxg_xpoa_stuff
d86eb17
@subwaystation
deactivate consensus graph
71c767a
@subwaystation
update to the most recent PGGB Dockerfile
2faea2b
@subwaystation
seqwish_sparse_factor
1a4e6c8
@subwaystation
update default values in nextflow.config
f99cefa
@subwaystation
added vcfwave step in vg_deconstruct
ec46421
@subwaystation
check for input indices and create them on the fly if required
a5379b9
@subwaystation
help message correction
5d14f7d
@subwaystation
if you happy and you know it clap your hands!
45eb867
@subwaystation
make the CI happy
2e022b5
@subwaystation
bring schema up to date
d49b11f
@subwaystation
bring schema up to date
9173fc5
@subwaystation
update help message
a2247ba
@subwaystation
another bug fix
44e5943
@subwaystation
Merge pull request #84 from nf-core/wake_me_up_when_september_ends
d3fc78c 
Wake me up when september ends
@subwaystation
Update README.md
d74f0dc
@subwaystation
Update README.md
e362316
@subwaystation
seqwish_groovey_magic
ca551b1
@subwaystation
Merge pull request #85 from nf-core/seqwish_groovey_magic
03775f1 
seqwish_groovey_magic
@subwaystation
odgi sort/layout power up
59e348f
@subwaystation
Merge pull request #86 from nf-core/odgi_sort_layout_power_up
34149c6 
odgi sort/layout power up
@subwaystation
update Dockerfile to use the most recent biwflambda update
d45e6d9
@subwaystation
Merge pull request #87 from nf-core/biwflambda
8070f46 
update Dockerfile to use the most recent biwflambda update
@subwaystation
diagnostic vizzz
985df21
@subwaystation
Merge pull request #23 from nf-core/diagnostic_summarized_viz
2149fc1 
Diagnostic summarized viz
@subwaystation
Merge pull request #88 from nf-core/diagnostic_summarized_viz
4d94b22 
diagnostic vizzz
@subwaystation
update wfmash for better short/medium sequence alignment
288c95c
@subwaystation
update CI
ae292d7
@subwaystation
Merge pull request #89 from nf-core/wfmash_power_up
a9003c0 
 update wfmash for better short/medium sequence alignment
@subwaystation
integrate gfaffix bugfix and wfmash update via Dockerfile
8fab77d
@FriederikeHanssen
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FriederikeHanssen commented Apr 20, 2023 •
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Reminder for myself/core: make nf-core the main repo before the release

@subwaystation subwaystation mentioned this pull request Jun 14, 2023
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@subwaystation
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Closing this in favour of #128.

@heuermh heuermh deleted the a_brave_new_world branch February 22, 2024 16:14
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3 participants
@subwaystation @FriederikeHanssen @mirpedrol