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phaseimpute first release (v1.0.0) #142

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phaseimpute first release (v1.0.0) #142

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@atrigila atrigila commented Oct 29, 2024 •
edited by LouisLeNezet
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First release of PhaseImpute 1.0.0 Black Labrador

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/phaseimpute branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

LouisLeNezet and others added 30 commits June 13, 2024 12:58
@LouisLeNezet
Add check for all imputation tools
8684f31
@LouisLeNezet
Update snapshot
b81c002
@LouisLeNezet
Set yml to 2 indent
8964fe2
@LouisLeNezet
Merge pull request #88 from LouisLeNezet/multiqc
20956e6 
Multiqc
@LouisLeNezet
Add header to samtools coverage stub
ad09829
@LouisLeNezet
Add script and update metromap
0127933
@LouisLeNezet
Add freq parameter and fix phasing
1c0d5b2
@LouisLeNezet
Add patch shapeit5
f820a43
@LouisLeNezet
Fix linting
1a367f5
@LouisLeNezet
Fix chunk generation
028773f
@LouisLeNezet
Update main.nf
a6c1f91
@LouisLeNezet
Reverse modification
277cee5
@LouisLeNezet
Add panelprep to metromap
3e3b140
@LouisLeNezet
Reverse change
29d6450
@LouisLeNezet
Update documentation
4b154d2
@LouisLeNezet
Add freq parameter and fix phasing
b996e7e
@LouisLeNezet
Add patch shapeit5
f68f8ef
@LouisLeNezet
Fix linting
c27c6f2
@LouisLeNezet
Fix chunk generation
57e06a6
@LouisLeNezet
Add parameter sim_by_chr and dinamically publish downsampled file
c843cb8 
USe samtools depth instead of coverage
@LouisLeNezet
Simplify channels creations
53d0a1f
@LouisLeNezet
Add freq parameter and fix phasing
fef294e
@LouisLeNezet
Add patch shapeit5
870fa07
@LouisLeNezet
Update metro map
5d281ac
@LouisLeNezet
Update metro map
25116be
@LouisLeNezet
Update image and README
0602cf9
@LouisLeNezet
Update README
537840e
@LouisLeNezet
Update metro map
4888c17
@LouisLeNezet
Lint modules.json
5679f7f
@LouisLeNezet
Fix merge error
aadc7b8
LouisLeNezet and others added 27 commits November 17, 2024 21:36
Reorder snap
93bd9ba
@LouisLeNezet
Merge pull request #160 from LouisLeNezet/documentation
c8e73e8 
Improve documentation
@LouisLeNezet
Merge branch 'dev' into fulltest_only
0e47798
@LouisLeNezet
Fix config
04a12c2
@LouisLeNezet
Update pluginsplit
8c1fff6
@LouisLeNezet
Fix splitting operation
8a7f9a1
@LouisLeNezet
Fix splitting operation
7846c23
@LouisLeNezet
Fix splitting operation
2eb5f00
Update truth split
a2b15da
@LouisLeNezet
Merge branch 'dev' into config
a8600fc
Update snap
c1b7f1e
@LouisLeNezet
Update bcftools pluginsplit
eeb8037
Update modules
0bd49f0
Update vcf_split_bcftools
c1fd186
Add samples renaming for truth splitted files
cd450c3
Reset changes
2e54095
Reset changes
ca67cbb
Reset changes
46464eb
Update CHANGELOG
d3aac0c
@LouisLeNezet
Merge pull request #161 from LouisLeNezet/config
e58c7e6 
Update VCF_SPLIT_BCFTOOLS
@LouisLeNezet
Merge branch 'dev' into fulltest_only
6ba6eba
Update snapshot
f8c01ac
Update snapshot
10d95fe
@LouisLeNezet
Merge pull request #158 from LouisLeNezet/fulltest_only
69badc3 
Reduce computational time of AWS megatest
@LouisLeNezet
Fix fasta index usage with igenome
a38adfa
@LouisLeNezet
Update CHANGELOG
aa55dfb
@LouisLeNezet
Merge pull request #162 from LouisLeNezet/fasta_index
d092479 
Fix fasta index usage with `genomes` parameter
@sofstam sofstam self-requested a review November 25, 2024 15:38
sofstam
sofstam reviewed Nov 27, 2024
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Nice work! I tried to understand the pipeline as much as possible. Here comes some questions and suggestions.

.github/CONTRIBUTING.md Show resolved Hide resolved
.github/CONTRIBUTING.md Show resolved Hide resolved
.github/CONTRIBUTING.md Show resolved Hide resolved
.github/CONTRIBUTING.md Show resolved Hide resolved
CHANGELOG.md

## v1.0dev - [date]
## v1.0.0 - Black Labrador [2024-10-28]
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Good to adjust this date to the actual release date.

docs/usage.md Show resolved Hide resolved
docs/usage.md Show resolved Hide resolved
subworkflows/local/bam_gl_bcftools/main.nf Show resolved Hide resolved
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@LouisLeNezet LouisLeNezet mentioned this pull request Nov 28, 2024
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@sofstam sofstam sofstam left review comments

@LouisLeNezet LouisLeNezet LouisLeNezet left review comments

@jfy133 jfy133 jfy133 left review comments

@mazzalab mazzalab mazzalab left review comments

@mashehu mashehu mashehu approved these changes

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Labels
enhancement New feature or request
Projects
Hackathon October 2024
Status: In Progress
Milestone
v0.99.0
Development

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9 participants
@atrigila @LouisLeNezet @mashehu @mazzalab @jfy133 @sofstam @maxulysse @nf-core-bot @hemanoel