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🔖 release v0.6.2#79

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bunop wants to merge 95 commits intomastercnr-ibba/nf-resequencing-mem:masterfrom devcnr-ibba/nf-resequencing-mem:devCopy head branch name to clipboard

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Commits on Apr 11, 2024

• ♻️ display current chrom with samtools/depth

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Commits on Jul 11, 2024

• ⬆️ upgrade picard/markduplicates module

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• 📝 update changelog

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• 💚 attempt to fix CI tests

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• 🔀 Merge pull request #78 from cnr-ibba/issue-77

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Commits on Jan 7, 2025

• 🔧 test profile using remote input

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• 📝 update README

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• 🐛 fix test file URLs

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• 📝 simplify documentation

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• 👷 update the GitHub actions

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• 💚 attempt to update nf-core tools used in linting workflow

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Commits on Jan 8, 2025

• 🚨 fix issues related to linter

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• 🔧 update the .nf-core.yml configuration file

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• 🔀 Merge pull request #83 from cnr-ibba/issue-81

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• 🚨 attempt to solve linter warning

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• 💚 attempt to fix download pipeline workflow

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• 💚 attempt to fix download pipeline workflow

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• 👷 remove conda tests from CI

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Commits on Jan 9, 2025

• ✨ pristine institutional config

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• 🐛 add missing institutional configuration

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Commits on Jan 13, 2025

• 🙈 update gitignore

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• ✨ concatenate vcf chunks by chromosomes

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Commits on Jan 14, 2025

• ➕ add bcftools/sort dependency

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• ♻️ minor refactoring to nextflow schema

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• 📌 Update nextflow to version 24.04.0

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• ✨ add freebayes normalize step

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• 🐛 fix issues with module names and config

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• 🔧 configure prefix using modules.conf

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• 📝 update changelog

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Commits on Jan 15, 2025

• ➕ add bcftools/concat process

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• ✨ concatenate chromosome VCF

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• ♻️ refactor tabix/tabix steps

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• 🚨 fix issues with linter

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Commits on Jan 16, 2025

• 🐛 fix issue with institutional configuration

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• 🔥 drop the gitpod profile

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• 📝 update README

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• 🔀 Merge pull request #84 from cnr-ibba/issue-76

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• ✨ add custom options for freebayes

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• 🔀 Merge pull request #85 from cnr-ibba/issue-80

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Commits on Jan 20, 2025

• 🚚 move REMOVE_OVERLAP into CRAM_FREEBAYES_PARALLEL workflow

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• ✨ start pipeline_initialization subworkflow

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• 🚚 move stuff in workflow

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• ⬆️ update MultiQC module

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• ⬆️ update snpeff/download

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• ⬆️ update snpeff/snpeff

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• 🔥 remove REMOVE_OVERLAP

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• 🔧 refactor modules.config

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• 🔧 pin snpeff/download and snpeff/snpeff

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• ⬆️ update modules

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• 🚨 solve issues with linters

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Commits on Jan 21, 2025

• ⬆️ upgrade bcftools-based modules

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• 🐛 fix conda container declaration in local modules

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• 🚨 attempt to solve issues with linters

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• 👷 update CI files

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Commits on Jan 22, 2025

• ⬆️ update freebayes container

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• 💩 attempt to fix FREEBAYES_NORM step

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• 🐛 fix freebayes container version

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• 🐛 fix process.shell in nextflow.config

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• ♻️ pass indexes between subworkflows

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• 🚨 ignore diff files with prettier

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• 🔀 Merge branch 'issue-86' into issue-88

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• 🔧 relax bcftools normalization parameters

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• 🚨 ignore diff file with .editorconfig

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• ✨ replace vcfallelicprimitives with vcfwave

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Commits on Jan 31, 2025

• 🔧 using a custom container for vcfwave

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• 🚨 fix issue related with linter

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• ⬆️ upgrade nf-core version

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Commits on Feb 3, 2025

• 🔀 Merge pull request #87 from cnr-ibba/issue-86

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• 🔀 Merge pull request #89 from cnr-ibba/issue-88

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• ♻️ update vcfwave version

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• 🚚 rename BCFTOOLS_CONCAT in NORMALIZED_CONCAT in main workflow

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• 🔥 remove cnr-ibba/bcftools/concat

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• 🚚 rename FREEBAYES_CONCAT as CONCATENATE_CHROMS

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• ✨ concatenate freebayes results if required

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• ♻️ annotate concatenated vcf file

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• 🎨 fix code format

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• ✨ skip normalization with a parameter

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Commits on Feb 4, 2025

• ✨ test for gvcf related parameters

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• 📝 update README

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Commits on Feb 5, 2025

• ⏪ Revert "♻️ update vcfwave version"

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• 🚨 fix issues related with linter

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• 🔀 Merge pull request #91 from cnr-ibba/issue-90

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• 🚚 rename FREEBAYES_NORMALIZE subworkflow into NORMALIZE_VCF

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• 🔧 define schema for normalization workflow

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• 💩 add normalization workflow to be called with -entry option

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Commits on Feb 7, 2025

• ✨ support normalization conditional workflow

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• 🔥 enforce nextflow schema and remove checks from code

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• 📝 update changelog

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Commits on Feb 10, 2025

• 🔀 Merge pull request #93 from cnr-ibba/issue-92

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