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Release 3.0 #238

Merged
merged 353 commits into from
Mar 20, 2023
Merged

Release 3.0 #238

merged 353 commits into from
Mar 20, 2023

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ggabernet
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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/airrflow 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).

ggabernet and others added 30 commits November 18, 2022 16:10
@ggabernet
save metadata table
b012477
@ggabernet
join meta after scqc process
6ff9c29
@ggabernet
clonal analysis with meta
1bac309
@ggabernet
find threshold update
bce3e31
@ggabernet
define clones by group
f8df4ad
@ggabernet
airr compliant fastq samplesheets
b1a08d5
@ggabernet
organize params
17cf431
@ggabernet
test validate input airr
db7fb15
@ggabernet
add workflow overview plot
b727c48
@ggabernet
add metro map
047ddde
@ggabernet
update meta input
af071d3
@ssnn-airr
added min_n for estimateAbundance
f4d7031
@ssnn-airr
oops
346b72c
@ggabernet
updated docs samplesheet fastq
365a6b7
@ssnn-airr
oops
4fdc619
@ssnn-airr
back to use nf-core test dbs
fa86bd1
@ggabernet
add mandatory fields to check samplesheet
6c06764
@ggabernet
add input docs
e068a3d
@ggabernet
implement define clones per clone group and report for all
d1c1b36
@ggabernet
update modules config
a19a0ba
@ggabernet
fix test profiles
3dab5ac
@ggabernet
fix subject_id parsing
b893196
@ssnn-airr
add log for file size report
ed20849
@ggabernet
add changeo label
9a6dea6
@ssnn-airr
trying to add convertdb log
51f2d75
@ssnn-airr
updated log file name
764aa12
@ssnn-airr
trying to add convertdb logs
c73aeaa
@ssnn-airr
fixed input order
885f576
@ggabernet
Merge pull request #205 from ggabernet/enchantr-400
16facd1 
New changes towards Enchantr 0.0.5
@ssnn-airr
merge enchantr-400
0a8a6e0
FriederikeHanssen and others added 20 commits March 15, 2023 18:06
@FriederikeHanssen
update aws paths
efef498
@FriederikeHanssen @ggabernet
Update conf/test_full.config
81e5d4e 
Co-authored-by: Gisela Gabernet <[email protected]>
@ewels
Merge pull request #247 from FriederikeHanssen/aws_paths
f06e19a 
update aws paths
@ggabernet
Merge pull request #245 from ggabernet/dev
a09d310 
Add missing module versions
@ggabernet
rm single_cpu label
2fb65a1
@ggabernet
add docstring immcantation label
1b4d145
@ggabernet
rm single_cpu label
fc61834
@ggabernet
exit 1 change to error
f0f5949
@ggabernet
Add author and licenses to bin scripts
dc35a93
@ggabernet @louperelo
Update nextflow_schema.json
708f4f3 
Co-authored-by: Louisa <[email protected]>
@ggabernet @louperelo
Update README.md
214ed65 
Co-authored-by: Louisa <[email protected]>
@ggabernet @louperelo
Update README.md
a7b122e 
Co-authored-by: Louisa <[email protected]>
@ggabernet @louperelo
Update README.md
c107b37 
Co-authored-by: Louisa <[email protected]>
@ggabernet @louperelo
Update README.md
ac72901 
Co-authored-by: Louisa <[email protected]>
@ggabernet @louperelo
Update README.md
7ab77f7 
Co-authored-by: Louisa <[email protected]>
@ggabernet @louperelo
Update nextflow_schema.json
2cac062 
Co-authored-by: Louisa <[email protected]>
@ggabernet
update test profile description
a41e633
@ggabernet
update docs
752c7aa
@ggabernet
Merge branch 'dev' of https://github.com/nf-core/airrflow into dev
d6e95d6
@ggabernet
update changelog
8c6c91d
@ggabernet
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Thanks so much @adamrtalbot and @louperelo for your very detailed reviews! I've applied most of your review comments on this separate PR: #248

Some answers to some more general comments too:

  • Regarding porting local modules to nf-core modules. This is something that should be done but it is no small feat. None of them exist in nf-core/modules and there's also no test data for any of them. Therefore I would like to get this release out and then focus on porting modules to nf-core.
  • Regarding the usage.docs, the new functionality has been updated accordingly there already.

louperelo
louperelo approved these changes Mar 16, 2023
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looks good to me

louperelo
louperelo approved these changes Mar 16, 2023
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Looks all good to me.

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@ggabernet ggabernet merged commit 2c73167 into master Mar 20, 2023
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@louperelo louperelo louperelo approved these changes

@adamrtalbot adamrtalbot adamrtalbot approved these changes

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@ggabernet @adamrtalbot @louperelo @ssnn-airr @nf-core-bot @dladd @FriederikeHanssen @ewels