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🔖 release v0.6.0#62

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bunop merged 62 commits intomastercnr-ibba/nf-resequencing-mem:masterfrom devcnr-ibba/nf-resequencing-mem:devCopy head branch name to clipboardApr 8, 2024

+4,939-1,194

Commits

Commits on Mar 14, 2024

• 💥 deal with CRAM using nf-core subworkflow

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Commits on Mar 15, 2024

• 👷 update linting workflows

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• 💚 add missing configuration file

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• 🔧 add pre-commit config

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• 🔀 Merge pull request #61 from cnr-ibba/issue-58

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• 🔀 Merge branch 'dev' into issue-9

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• ♻️ fix freebayes_parallel subworkflow dependencies

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• ➖ remove bamaddrg dependency

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• ➖ remove nf-core bcftools/concat

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• 🔧 remove bamaddrg configuration

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• 🔥 remove unused modules from resequencing-mem workflow

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• 🚨 patch bwa module and pass test

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• 🐛 fix read groups information in bwa/mem step

  bunop

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Commits on Mar 18, 2024

• ⚡ attempt to call markduplicates and generate cram

  bunop

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• ♻️ rename bam and bai with cram and crai in workflows

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• 🚨 deal with linter issues

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Commits on Mar 21, 2024

• ➕ add samtools/depth module

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• ✨ calculate total coverage for all samples

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• 🚚 move freebayes_parallel subworkflow to a local subworkflow

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• 🚨 patch samtools/depth module

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• 💥 change freebayes/splitbam module

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• 🚚 move nf-core subworflows to local workflows

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Commits on Mar 22, 2024

• Resolved use of existing genome_bwa_index

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• 📝 update documentation

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• 🚚 move freebayes_splitbam into freebayes_splitcram

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• ✨ save cram output as a result

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• 🐛 fix split_ref_by_depth.py when deal with multiple chromsomes

  bunop

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• 🐛 fix extended region case

  bunop

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• ✨ introduce an overlap between regions while splitting

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• 🔀 Merge branch 'issue-9' into issue-9.1

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Commits on Mar 24, 2024

• 🔥 remove unused file

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• ⚡ tune markduplicate step

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Commits on Mar 25, 2024

• 🐛 fix issue in split_ref_by_depth

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• ♻️ refactor split_ref_by_depth

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• 🔀 Merge pull request #66 from cnr-ibba/issue-9.1

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Commits on Mar 26, 2024

• 🐛 fix another issue in split_ref_by_depth

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• ➕ add snpEff modules

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• ✨ start SNPEFF_ANNOTATE local subworkflow

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• ✨ annotate variants with SnpEff

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• 🐛 fix issue when SnpEff is not executed

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• 📝 update docs

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Commits on Mar 27, 2024

• 🔧 tune resources usage

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• 🔀 Merge pull request #63 from cnr-ibba/issue-9

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• 🔀 Merge branch 'dev' into issue-59

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Commits on Mar 28, 2024

• ✨ compress SnpEff output

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• ✨ execute SnpEff with a custom database

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• 🐛 fix default SnpEff step

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• 📝 update docs

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• 🔀 Merge pull request #67 from cnr-ibba/issue-59

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• 🔧 update MULTIQC config

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• ♻️ minor fixes

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• ⬆️ upgrade MULTIQC module

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• 🔀 Merge pull request #68 from cnr-ibba/issue-60

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• ⬆️ upgrade dependencies

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• 🐛 fix issue related to updated samtools/coverage

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• ⬆️ upgrade bwa/mem

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• 🔧 change configuration to support latest bwa/mem

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• ⬆️ upgrade picard/markduplicates

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Commits on Apr 4, 2024

• 📝 update CHANGELOG

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• 🔀 Merge pull request #69 from cnr-ibba/issue-64

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• 🔖 release v0.6.0

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Commits on Apr 8, 2024

• 📝 update README

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