[Do not merge!] Pseudo PR for first release #155

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mashehu wants to merge 1151 commits intoTEMPLATEfrom dev

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Commits on Oct 10, 2024

Merge pull request #117 from atrigila/issue_114
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Commits on Oct 11, 2024

Nf core template merge 3.0.1 (#128 )

LouisLeNezet
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nf-core-bot
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Important! Template update for nf-core/tools v3.0.2 (#129 )

nf-core-bot
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LouisLeNezet
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Commits on Oct 15, 2024

Normalization as optional and publishing improvment (#131 )

LouisLeNezet
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atrigila
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Commits on Oct 17, 2024

Add animated metro map (#134 )

LouisLeNezet
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LouisLeNezet
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Commits on Oct 29, 2024

Commits on Nov 5, 2024

Commits on Nov 6, 2024

Update language server
LouisLeNezet
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Remove input from input initialisation
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Update changelog
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Fix numbering batch
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Update nf-test modules
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Fix fulltest
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Update nf-test
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Update nf-test
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Update nf-test
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Remove .view()
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Set resourceLimits
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Fix region processed with subset
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Set resourceLimits
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Update nf-test
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change how to install nf-test
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remove tsv that is not produced anymore
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remove repeated information
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give higher level heading to tools, fix grammar
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add groovylang
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delete tags.yml
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align
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fix patterns in schema
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revert setup nf-test
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test sharding strategy in ci
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Revert "test sharding strategy in ci"
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make contributing.md same as template
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fix typo in chrX chr39
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Commits on Nov 7, 2024

Update nf-test
LouisLeNezet
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Fix function validateInputBatchTools
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Add null return
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Remove println
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Update CHANGELOG
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Commits on Nov 8, 2024

Commits on Nov 10, 2024

update image with white background
atrigila
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improve introduction flow
atrigila
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use setup nf-test
atrigila
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Change chunk model initialisation
LouisLeNezet
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Update nextflow_schema.json

atrigila
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LouisLeNezet
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Add nf-test for chunk model
LouisLeNezet
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Reduce spec of PR
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Merge pull request #157 from LouisLeNezet/chunk_model
LouisLeNezet
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remove spaces
atrigila
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Merge branch 'adress_review_comments' of https://github.com/atrigila/phaseimpute into adress_review_comments
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Merge branch 'dev' into fulltest
LouisLeNezet
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modify diagram
atrigila
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Commits on Nov 11, 2024

Merge pull request #153 from LouisLeNezet/fulltest
LouisLeNezet
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Reduce features of fulltest

LouisLeNezet
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LouisLeNezet
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Update changelog
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Check for multiple sample before splitting
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Commits on Nov 12, 2024

Fix case if empty
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Update snapshot phasing sbwf
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Update CHANGELOG
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Update config
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Add query version
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Remove unecessary sbwf inclusion
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Update changelog and add dependencies
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Fix window size
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Fix name output suffix
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Update config
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Fix small naming
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Clean multiqc
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Update output.md
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Update nf-test and snapshot
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Fix config import order
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Commits on Nov 13, 2024

Reset changes
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Update pluginsplit
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Update test
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Update changelog and remove bcftools query from config
LouisLeNezet
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Update output.md and remove bcftools query from config
LouisLeNezet
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Update nf-test sbwf
LouisLeNezet
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Commits on Nov 17, 2024

update diagram
atrigila
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Merge pull request #156 from atrigila/adress_review_comments
atrigila
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Update docs/output.md

LouisLeNezet
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atrigila
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Merge branch 'dev' into fulltest_only
LouisLeNezet
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Update output and CHANGELOG
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Reset changes
LouisLeNezet
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Reset pluginsplit
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Fix pluginsplit
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Add back lenient mode in PR
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Change resourceLimits
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Set back testquality
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Set to AllSamples.txt
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Change resourceLimits
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Update vcf_split_bcftools
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Reset VCF_SPLIT_BCFTOOLS
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Add chunks size config
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Update CHANGELOG
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Update snapshot
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Update snapshot
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Reset change
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Reset change
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Update snapshot
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Fix snapshot
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Improve output organisation
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Reorder snap
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Commits on Nov 21, 2024

Update bcftools pluginsplit
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Commits on Nov 22, 2024

Update modules
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Update vcf_split_bcftools
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Add samples renaming for truth splitted files
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Reset changes
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Reset changes
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Reset changes
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Commits on Nov 23, 2024

Update CHANGELOG
LouisLeNezet
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Merge pull request #161 from LouisLeNezet/config
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Merge branch 'dev' into fulltest_only
LouisLeNezet
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Update snapshot
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Update snapshot
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Commits on Nov 24, 2024

Merge pull request #158 from LouisLeNezet/fulltest_only
LouisLeNezet
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Commits on Nov 25, 2024

Commits on Nov 28, 2024

Commits on Nov 29, 2024

Change background
LouisLeNezet
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Commits on Dec 2, 2024

Merge pull request #164 from LouisLeNezet/dev
LouisLeNezet
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Update metromap and logo
LouisLeNezet
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Improve fulltest

LouisLeNezet
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LouisLeNezet
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Update CHANGELOG

LouisLeNezet
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LouisLeNezet
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Revert extension change

LouisLeNezet
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LouisLeNezet
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Revert extension change

LouisLeNezet
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LouisLeNezet
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Fix multiqc file names
LouisLeNezet
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Update CHANGELOG
LouisLeNezet
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Update snapshot
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Update gawk

LouisLeNezet
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LouisLeNezet
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Update CHANGELOG

LouisLeNezet
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LouisLeNezet
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Fix configuration

LouisLeNezet
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LouisLeNezet
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Update sample samplesheet

LouisLeNezet
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LouisLeNezet
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Fix input truth vcf usage

LouisLeNezet
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LouisLeNezet
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Fix glimpse2 concordance usage

LouisLeNezet
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LouisLeNezet
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Reverse modification
LouisLeNezet
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Commits on Dec 4, 2024

Update glimpse2 concordance
LouisLeNezet
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Update java version
LouisLeNezet
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Update CHANGELOG.md
LouisLeNezet
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Update metromap
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Update metromap
LouisLeNezet
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Commits on Dec 5, 2024

Update metromap
LouisLeNezet
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Commits on Dec 6, 2024

Merge pull request #163 from LouisLeNezet/awstest
LouisLeNezet
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Commits on Dec 7, 2024

Update metromap
LouisLeNezet
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Merge branch 'dev' into metromap
LouisLeNezet
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Add animated metromap
LouisLeNezet
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Commits on Dec 8, 2024

Update legend
LouisLeNezet
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Commits on Dec 9, 2024