8000 Release 2.1.0 by skrakau · Pull Request #223 · nf-core/mag · GitHub
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Merged
merged 59 commits into from
Jul 29, 2021
Merged

Release 2.1.0 #223

merged 59 commits into from
Jul 29, 2021

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skrakau
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@skrakau skrakau commented Jul 27, 2021 •
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  • add bin abundance estimation and generation of heatmap with abundances across samples
  • publish Prodigal bin annotations obtained from BUSCO run
  • template update
  • update overview figure
  • use assembly reproducibility setting for full-size test profile

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](https://github.com/nf-core/mag/tree/master/.github/CONTRIBUTING.md)
    • If necessary, also make a PR on the nf-core/mag 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).

skrakau and others added 30 commits June 1, 2021 14:01
@skrakau
Bump version 2.1.0dev
93dcedc
@skrakau
Merge pull request #210 from skrakau/bump_2.1.0dev
167f95d 
Bump version 2.1.0dev
@skrakau
Add computing average mag depths
8356539
@skrakau
Update container comment
04594b6
@skrakau
Update comments
a6fbe09
@skrakau
Adjust samples names for bin depths
6ecb87d
@skrakau
Fix sep for writing bin depths
2a56820
@skrakau
Add description of generated bin depths to docs
1d9f506
@skrakau
Adjust help of get_mag_depths.py
a383048
@skrakau
Add generation of bin depths summary
aa226bf
@skrakau
Change default publish_id for mag_depths process
18e9f2b
@skrakau
Merge bin depths into bin_summary.tsv
2393c65
@skrakau
Renamed process MERGE_QUAST_BUSCO_GTDBTK to BIN_SUMMARY
c16a87b
@skrakau
Rename depths columns in bin_summary.tsv
51c1102
@skrakau
Update output.md for new bin_depths_summary.tsv
6266d68
@skrakau
Increase mem for process MAG_DEPTHS
7135cc0
@skrakau
Adjust bin_summary.tsv description in output.md for depths
50876fa
@skrakau
Update CHANGELOG
5d94520
@skrakau
Merge pull request #212 from skrakau/comp_mag_abundances
19ab05e 
Compute bin depths
@skrakau
Add first version of bin depths heatmap
c8b2ce6
@skrakau
Add group information to clustered heatmap
a27fba9
@skrakau
Compute median bin depths instead of mean
1f99176
@skrakau
Update CHANGELOG
7fcdb20
@skrakau
Create bin abundance heat maps only when > 2 samples where mapped
dd4daaa
@skrakau
Add bin abundance heatmap description to output.md
560ebd8
@skrakau
Center headmap color scale
c7724b2
@skrakau
Merge pull request #214 from skrakau/plot_mag_abundences
01384ca 
Plot bin abundances as heat map
@KevinMenden
Template update for nf-core/tools version 2.0
42bd797
@nf-core-bot
Template update for nf-core/tools version 2.0.1
a15c2e4
@skrakau
Publish genes predicted with Prodigal in BUSCO process
0b0c187
@skrakau skrakau requested review from ggabernet and d4straub July 27, 2021 12:24
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github-actions bot commented Jul 27, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2fecf1f

+| ✅ 135 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '2.1.0'
  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-07-28 20:12:57

@skrakau
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skrakau commented Jul 27, 2021
8000

why is there a warning saying:
nextflow_config - Config manifest.version should end in dev: '2.1.0' ?

d4straub
d4straub approved these changes Jul 27, 2021
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@d4straub d4straub left a comment •
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Nice!

Edit:

why is there a warning saying:
nextflow_config - Config manifest.version should end in dev: '2.1.0' ?

Because its the dev branch? no worries!

ggabernet
ggabernet approved these changes Jul 27, 2021
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Looks good to me!

@ggabernet
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why is there a warning saying:
nextflow_config - Config manifest.version should end in dev: '2.1.0' ?

Yeah I think this is actually a bug, it should not give out this warning for PRs from dev to master

@skrakau
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skrakau commented Jul 27, 2021

Thanks @d4straub and @ggabernet !

@skrakau skrakau closed this Jul 28, 2021
@skrakau skrakau reopened this Jul 28, 2021
@skrakau skrakau merged commit d4f00bc into master Jul 29, 2021
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@ggabernet ggabernet ggabernet approved these changes

@d4straub d4straub d4straub approved these changes

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@skrakau @ggabernet @d4straub @KevinMenden @nf-core-bot
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