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phaseimpute first release (v1.0.0) #142

Merged
merged 1,156 commits into from
Dec 9, 2024
Merged

phaseimpute first release (v1.0.0) #142

merged 1,156 commits into from
Dec 9, 2024

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atrigila
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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).

atrigila and others added 20 commits August 31, 2024 21:10
@atrigila
fix csv
f348eda
@atrigila
Merge pull request #119 from atrigila/test_dog
e7d34a4 
Improve tests in dog genome
@atrigila
update changelog
c836b09
@atrigila
add pdiff to nf-test
0832ad1
@atrigila
Merge branch 'dev' into issue_114
04dc761
@atrigila
update nextflow version in ci
ddaea17
@atrigila
fix linting
36037bd
@atrigila
Merge pull request #117 from atrigila/issue_114
a2653ed 
change output directory
@LouisLeNezet @nf-core-bot
Nf core template merge 3.0.1 (#128)
c007e41 
* Template update for nf-core/tools version 3.0.0

* Template update for nf-core/tools version 3.0.1

* Update template_version_comment.yml

* Update template_version_comment.yml

* Add title to usage files

* Remove old way igenomes config

* Update main.nf and utils nf-core sbwf

* Update schema json

* Fix linting

* Update validation snap

---------

Co-authored-by: nf-core-bot <[email protected]>
@nf-core-bot @LouisLeNezet
Important! Template update for nf-core/tools v3.0.2 (#129)
87f537c 
* Template update for nf-core/tools version 3.0.0

* Template update for nf-core/tools version 3.0.1

* Template update for nf-core/tools version 3.0.2

* Update sha

---------

Co-authored-by: Louis Le Nezet <[email protected]>
@LouisLeNezet @atrigila
Normalization as optional and publishing improvment (#131)
0a25c1c 
* New dev

* Rename function

* Fix function

* Update workflow name

* Update tests

* Update function usage

* Update tests snapshot

* Update changelog

* Change phased to phase

* Update documentation

* Update snapshot

* Update publishing panel

* Update test

* Update docs/usage.md

Co-authored-by: Anabella Trigila <[email protected]>

---------

Co-authored-by: Anabella Trigila <[email protected]>
@LouisLeNezet
Add animated metro map (#134)
a746a17 
* Update workflow metro map

* Update metro map

* Update metro map and add animation

* Improve timing svg

* Update README.md

---------

Co-authored-by: LouisLeNezet <[email protected]>
@LouisLeNezet
Add batch support (#135)
a4f6618 
* Remove phase autodetect

* Aggregate glimpse1 bams, merge vcf

* Aggregate glimpse and quilt bams

* Add to conf

* Add fasta to quilt and keep vcf merged

* Add modules list_to_file

* Order called sample

* Take out GL computation from swf glimpse1

* Add bamlist to quilt and glimpse2

* Put stitch parameters preparation in stitch sbwf

* Add batch_size and group samples in main workflow

* Update config

* Update config

* Add validation of batch size and tools compatibility

* Update test workflow

* Add batch to metamap

* Update conf

* Fix bam regions map

* Use dot as separator

* Update test and Changelog

* Update docs

* Improve documentation

* Patch modified modules

* Order samples names in snaphot

* Update changelog

* Improve pipeline

* Order files before grouping and split output vcf

* Add validation to snapshot

* Update schema description

* Fix tags

* Add splitting by samples for each output

* Split validation truth set by sample

* Fix split

* Put in samples folder

---------

Co-authored-by: LouisLeNezet <[email protected]>
@LouisLeNezet
Update all nf-core modules (#139)
8fb7bf0 
* Update bcftools annotate

* Update bcftools concat

* Update bcftools convert

* Update bcftools index

* Update bcftools merge

* Update bcftools mpileup

* Update bcftools norm

* Update bcftools pluginsplit

* Update bcftools stats

* Update bcftools view

* Update bedtools makewindows

* Remove dumpsoftware

* Update gawk

* Update glimpse

* Update glimpse2

* Update gunzip

* Update quilt

* Update samtools

* Update shapeit5

* Update shapeit5

* Update stitch

* Update tabix

* Update vcflib

* Fix linting

* Update pluginsplit
@LouisLeNezet
Update workflows
252d63a
@LouisLeNezet
Simplify chromosome number checking
d2fa7f8
@LouisLeNezet
Add error if contigs intersection is empty
9c1006a
@LouisLeNezet
Add parameter for max number of chromosomes showed
a0a673c
@LouisLeNezet
Add log info
e9984d1
@LouisLeNezet
Improve logging information
feecec1
LouisLeNezet and others added 5 commits October 29, 2024 10:09
@LouisLeNezet
Update changelog
af3d541
@LouisLeNezet
Fix error
35a98f7
@LouisLeNezet
Fix conda environment
abd697f
@atrigila @LouisLeNezet
Check guidelines for release and add corrections (#132)
e351bb3 
* typo fixes in readme

* remove some to-dos

* remove todos, add bibliography

* add conditional detection of tools

* add missing tools to citations

* add conditional params

* add release name and date

* bump versions

* add contributors and reviewers

* Update README.md

* Update README.md

* Update README.md

---------

Co-authored-by: Louis LE NEZET <[email protected]>
@atrigila
Merge pull request #143 from LouisLeNezet/fix_checkchr
262290e 
Fix checkchr
@atrigila
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We are waiting on the community input on what to do with failing conda tests with the java.nio.channels.OverlappingFileLockException error.

@LouisLeNezet
Conda check removed and seed parameters added for QUILT (#146)
679f50e 
* Remove conda from PR test

* Add seed for stitch and quilt

* Bump version in nf-core yml

* Update changelog
@LouisLeNezet LouisLeNezet marked this pull request as ready for review October 29, 2024 12:58
LouisLeNezet and others added 29 commits December 2, 2024 19:03
@LouisLeNezet
Improve fulltest
a89cf5f
@LouisLeNezet
Update CHANGELOG
a9eafb3
@LouisLeNezet
Revert extension change
79b7dfb
@LouisLeNezet
Revert extension change
7a36d04
Fix multiqc file names
14d8aee
Update CHANGELOG
298296b
Update snapshot
21656bb
@LouisLeNezet
Update gawk
8d97f74
@LouisLeNezet
Update CHANGELOG
8e271b4
@LouisLeNezet
Fix configuration
1f6c784
@LouisLeNezet
Update sample samplesheet
98fbeaa
@LouisLeNezet
Fix input truth vcf usage
275d31d
@LouisLeNezet
Fix glimpse2 concordance usage
69306d9
Reverse modification
0d90bb2
Update glimpse2 concordance
9b630c3
Update java version
d1e289c
@LouisLeNezet
Update CHANGELOG.md
4c846d0
Update metromap
f932683
Update metromap
fba34d4
@LouisLeNezet
Update metromap
97b4a9b
@LouisLeNezet
Merge pull request #163 from LouisLeNezet/awstest
61c18f6 
Improve config and reduce fulltest
Update metromap
23ccd09
@LouisLeNezet
Merge branch 'dev' into metromap
4ab984a
Add animated metromap
8b55757
Update legend
397a4f4
@LouisLeNezet
Update metromap colors
55fa2b1
@LouisLeNezet
Update png
1054565
@LouisLeNezet
Update metromap
10c04e5
@LouisLeNezet
Merge pull request #165 from LouisLeNezet/metromap
b9d4f7d 
Update metromap and logo
@LouisLeNezet LouisLeNezet merged commit ac730dc into master Dec 9, 2024
31 of 37 checks passed
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Reviewers

@LouisLeNezet LouisLeNezet LouisLeNezet left review comments

@jfy133 jfy133 jfy133 left review comments

@mazzalab mazzalab mazzalab left review comments

@mashehu mashehu mashehu approved these changes

@sofstam sofstam sofstam approved these changes

Assignees

@atrigila atrigila

@LouisLeNezet LouisLeNezet

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

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