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Dev -> Master for 2.6 release #361

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drpatelh merged 102 commits intomasternf-core/viralrecon:masterfrom devnf-core/viralrecon:devCopy head branch name to clipboardMar 23, 2023

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Commits on Jul 13, 2022

• Bump pipeline version to 2.6dev

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• Merge pull request #319 from drpatelh/sync

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Commits on Aug 2, 2022

• Fixed problem with no annotation and duplicated lines

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Commits on Aug 8, 2022

• add biopython to conda env

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Commits on Aug 15, 2022

• Update modules/local/ivar_variants_to_vcf.nf

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• Update ivar_variants_to_vcf.nf

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Commits on Aug 19, 2022

• Update CHANGELOG.md

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• prettier linting

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• Merge pull request #323 from tavareshugo/patch-2

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Commits on Aug 23, 2022

• fixed StopIteration error

  

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• updated log counting behaviour

  

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• Merge pull request #1 from mattheww95/ivar_vcf_fix

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Commits on Aug 24, 2022

• Merge pull request #325 from BU-ISCIII/dev

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Commits on Aug 25, 2022

• Merge pull request #326 from mattheww95/master

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Commits on Aug 30, 2022

• Template update for nf-core/tools version 2.5

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Commits on Sep 1, 2022

• Template update for nf-core/tools version 2.5.1

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Commits on Oct 5, 2022

• Template update for nf-core/tools version 2.6

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Commits on Nov 29, 2022

• merge template

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• fix merge conflicts

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• fix merge conflicts

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• fix nexflow_schema.json

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• fix path to modules

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• update path in subworkflows

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• properly fix path

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• fix path to templates

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• black

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Commits on Nov 30, 2022

• Merge pull request #342 from maxulysse/dev

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• update artic version

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• add artic version update

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Commits on Dec 1, 2022

• Merge pull request #343 from tavareshugo/bump_artic

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Commits on Feb 23, 2023

• merge TEMPLATE

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Commits on Feb 24, 2023

• black

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• fix python script with black

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• restore docs

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• Merge pull request #355 from maxulysse/merge_template

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Commits on Mar 6, 2023

• Run nf-core modules update --all

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Commits on Mar 7, 2023

• Fix Illumina tests after updating modules/subworkflows

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• Fix ONT tests after updating modules/subworkflows

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• Update CHANGELOG

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• Update all modules again

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• Use channels as defaults for reference files

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Commits on Mar 8, 2023

• Merge pull request #359 from drpatelh/sync

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Commits on Mar 11, 2023

• Add tower.yml

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• Fix #349

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• Fix #320

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• Fix #316

  drpatelh

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• Add collect() where required after updating ref channels

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• Add collect() where required after updating ref channels

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• Fix syntax consistency

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• Update CHANGELOG

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• Add collect() where required after updating ref channels

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• Remove TODO statement

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• Bump versions for nf-core/modules

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• Revert unicycler version bump

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• Fix prettier

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• Run nf-core modules update --all after bumping versions

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Commits on Mar 12, 2023

• Merge pull request #360 from drpatelh/sync

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Commits on Mar 13, 2023

• Update CHANGELOG

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• Update CHANGELOG

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• Bump pipeline version to 2.6

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• Tidy up .nf-core.yml

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• Remove script now added to nf-core/fetchngs

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• Add software version changes to CHANGELOG

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• Fix PycoQC files not being published with correct name

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• Always provide reference data as value channels - Illumina

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• Always provide reference data as value channels - ONT

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• Do not evaluate params.gff for SNPEFF_BUILD

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• Merge pull request #362 from drpatelh/sync

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Commits on Mar 15, 2023

• update paths

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• update paths

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• Merge pull request #363 from FriederikeHanssen/aws_paths

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Commits on Mar 16, 2023

• Add custom function to replace MULTIQC_TSV_FROM_LIST process

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• Replace MULTIQC_TSV_FROM_LIST with custom function - ONT

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• Replace MULTIQC_TSV_FROM_LIST with custom function - Illumina

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• Merge branch 'dev' of https://github.com/nf-core/viralrecon into sync

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Commits on Mar 17, 2023

• Fix order of sections in MultiQC report

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• Remove --tracedir

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• Merge pull request #364 from drpatelh/sync

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Commits on Mar 19, 2023

• Create new folder on test-datasets for all samplesheets

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• Change S3 path to igenomes for kraken2 database

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• Merge pull request #365 from drpatelh/sync

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Commits on Mar 21, 2023

• Add credits to CHANGELOG

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• Use semantic versioning

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• Update all nf-core/modules and subworkflows

  drpatelh

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• Fix paths in subworkflows

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• Merge pull request #366 from drpatelh/fixes

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Commits on Mar 22, 2023

• add subway map

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• Update CHANGELOG.md

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• address some comments from @jfy133

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• Fix #368

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• Add more prominent warnings about using custom config to provide parameters

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• Reword warning

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• Update message in README and usage docs

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• Add main for consistency in subworkflow path

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Commits on Mar 23, 2023

• address more comments from @jfy133

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• address last comments from @jfy133

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• address final comments from @jfy133

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• Update lib/NfcoreTemplate.groovy

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• Change = to ~ everywhere - thanks for opening Pandora's box @jfy133

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• Change = to ~ everywhere - thanks for opening Pandora's box @jfy133

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• Merge pull request #367 from nf-core/subway_map

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• Merge pull request #370 from drpatelh/fixes

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