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1.0.0 - Ratzupaltuff #135

Merged
merged 534 commits into from
Aug 1, 2023
Merged

1.0.0 - Ratzupaltuff #135

merged 534 commits into from
Aug 1, 2023

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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 - 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 --outdir <OUTDIR>).
  • 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).

Towards a first release of the nf-core/pangenome pipeline. Fingers crossed :)

subwaystation and others added 30 commits December 14, 2022 11:45
@subwaystation
HOLIDAYgit add subworkflows/*!
fb226ca
@subwaystation
let's cheat
91a6139
@subwaystation
hmm
c156bca
@subwaystation
fix fai,gzi paths
5370b6e
@subwaystation
remove unecessary .view()
c93c9b9
@subwaystation
fix vg_deconstruct issues
fff9e58
@subwaystation
text communities and a more recent NXFv
461b2d6
@subwaystation
EOL
106fe2d
@subwaystation
remove dangling .view()
a204f7c
@subwaystation
update test parameters for faster runtime
0b668eb
@subwaystation
update test parameters for faster runtime
b00a322
@subwaystation
test new CI setup
f893c02
@subwaystation
maybe we can't go latest
7a659ed
@subwaystation
la vie est fantastique
c5eff66
@subwaystation
we want the matrix across parameters
77440ef
@subwaystation
force older Nextflow version
bf7ab00
@subwaystation
squeeze it!
fa85add
@subwaystation
fix --wfmash_only bug
ce0da3e
@subwaystation
subworkflow squeeze is ready :)
490f54e
@subwaystation
update help text and online parameter docs
a426db6
@subwaystation
Merge pull request #105 from nf-core/community
ba0cf69 
Community
@subwaystation
Merge pull request #28 from nf-core/dev
cea6a55 
Community update
@subwaystation
we have to copy the new python files
4ac12b7
@subwaystation
typo [skip ci]
e99d57b
@subwaystation
Merge pull request #29 from nf-core/dev
2d89940 
Update from Upstream
@subwaystation
Update README.md
27ddba6
@subwaystation
Merge pull request #30 from nf-core/dev
45757e2 
Update README.md
@nf-core-bot
Template update for nf-core/tools version 2.7.2
6a91abd
@subwaystation
enable trace.overwrite
e2ef284
@subwaystation
update pggb docker image
7f29118
@maxulysse
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maxulysse commented Jun 26, 2023 •
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Nope, how could I have done all of these in one commit using the github interface?

If you go in the Files changed tab, you can add a commit to batch and then batch commit several

heuermh
heuermh reviewed Jul 14, 2023
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modules/nf-core/wfmash/main.nf
$query_list \\
--threads $task.cpus \\
$paf_mappings \\
$args > ${prefix}.paf
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On start, wfmash options do not seem to have defaults

Wfmash Options
wfmash_block_length : null
wfmash_sparse_map : null

shows up as

Wfmash Options
wfmash_block_length N/A
wfmash_sparse_map N/A

in the MultiQC report, under nf-core/pangenome Workflow Summary

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@subwaystation subwaystation Jul 17, 2023 •
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I was also seeing this and was annoyed.
These parameters can be set, but if they are not set, they will be calculated based on other parameters later. So I am not sure what to do here.

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Because one should never set params.<PARAM> later.

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I see, haven't run into this before. Maybe drop a question on nf-core slack to see if anyone else might have a suggestion.

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https://nfcore.slack.com/archives/CE6SDBX2A/p1689605084916579

I tried, but no answer, yet.

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If I don't get an answer by the end of the week, I would resolve this conversation and continue the first release protocol.

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@maxulysse @mirpedrol Do you know more here maybe?

heuermh
heuermh reviewed Jul 14, 2023
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heuermh
heuermh reviewed Jul 14, 2023
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heuermh commented Jul 14, 2023

Ran -profile test,docker locally and did a quick review, will do a closer look this weekend

heuermh
heuermh reviewed Jul 14, 2023
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heuermh commented Jul 14, 2023

I see no blockers, only small doc changes 🎉

Would you like me to suggest changes or pull request against this branch?

@subwaystation
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@heuermh Suggest changes here would be cool!

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Thanks for the review @heuermh !

heuermh
heuermh approved these changes Jul 18, 2023
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subwaystation and others added 2 commits July 19, 2023 09:50
@subwaystation @heuermh
Update README.md
1001f65 
Co-authored-by: Michael L Heuer <heuermh@acm.org>
@subwaystation
update affiliations
52f6787
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I think If this is a first release, ask a core team member to activate the Zenodo functionality for this repository, which will be used to generate a DOI. is still missing here @FriederikeHanssen @maxulysse @heuermh.

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heuermh commented Jul 25, 2023

I think If this is a first release, ask a core team member to activate the Zenodo functionality for this repository, which will be used to generate a DOI. is still missing here

Per Slack, we're ready to go!

@subwaystation subwaystation merged commit 9fc8ccd into master Aug 1, 2023
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heuermh commented Aug 1, 2023

🎉

@subwaystation subwaystation mentioned this pull request Aug 3, 2023
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@heuermh heuermh heuermh approved these changes

@maxulysse maxulysse maxulysse approved these changes

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@subwaystation @maxulysse @mirpedrol @heuermh @nf-core-bot