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Dev -> Master for 2.5 release #315

Merged
merged 70 commits into from
Jul 13, 2022
Merged

Dev -> Master for 2.5 release #315

merged 70 commits into from
Jul 13, 2022

Commits on Mar 4, 2022

  1. Bump pipeline version to 2.5dev

    @drpatelh
    drpatelh committed Mar 4, 2022
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Commits on Mar 10, 2022

  1. Merge pull request #293 from drpatelh/bump 

    Bump pipeline version to 2.5dev
    @drpatelh
    drpatelh authored Mar 10, 2022
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Commits on Mar 15, 2022

  1. Template update for nf-core/tools version 2.3

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    nf-core-bot committed Mar 15, 2022
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Commits on Mar 23, 2022

  1. Template update for nf-core/tools version 2.3.1

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    nf-core-bot committed Mar 23, 2022
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Commits on Mar 24, 2022

  1. Template update for nf-core/tools version 2.3.2

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    nf-core-bot committed Mar 24, 2022
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Commits on Mar 31, 2022

  1. Fix merge conflicts

    @drpatelh
    drpatelh committed Mar 31, 2022
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  2. Update CHANGELOG after merging template updates

    @drpatelh
    drpatelh committed Mar 31, 2022
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  3. Fix template merge bug

    @drpatelh
    drpatelh committed Mar 31, 2022
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Commits on Apr 1, 2022

  1. Remove TODO statement in README

    @drpatelh
    drpatelh committed Apr 1, 2022
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  2. Remove retry logic from AWS actions

    @drpatelh
    drpatelh committed Apr 1, 2022
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  3. Add .prettierignore file

    @drpatelh
    drpatelh committed Apr 1, 2022
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  4. Fix ECLint

    @drpatelh
    drpatelh committed Apr 1, 2022
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  5. Merge pull request #301 from drpatelh/sync 

    Update CHANGELOG after merging template updates
    @drpatelh
    drpatelh authored Apr 1, 2022
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Commits on Apr 12, 2022

  1. Merge branch 'dev' of github.com:BU-ISCIII/viralrecon into dev

    @saramonzon
    saramonzon committed Apr 12, 2022
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  2. start reformat

    @saramonzon
    saramonzon committed Apr 12, 2022
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  3. draft reformat

    @saramonzon
    saramonzon committed Apr 12, 2022
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  4. vcf conversion and strand bias working

    @saramonzon
    saramonzon committed Apr 12, 2022
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Commits on Apr 13, 2022

  1. fixed bugs, finished first debugging

    @saramonzon
    saramonzon committed Apr 13, 2022
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  2. black linting

    @saramonzon
    saramonzon committed Apr 13, 2022
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  3. comments and function reordering

    @saramonzon
    saramonzon committed Apr 13, 2022
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  4. fix variants iterator

    @saramonzon
    saramonzon committed Apr 13, 2022
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  5. fixed bug in format field and last lines handling

    @saramonzon
    saramonzon committed Apr 13, 2022
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  6. minor fixed comment

    @saramonzon
    saramonzon committed Apr 13, 2022
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Commits on Apr 14, 2022

  1. updated changelog

    @saramonzon
    saramonzon committed Apr 14, 2022
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  2. Merge pull request #304 from BU-ISCIII/dev 

    Re-factor code (proposal) for ivar_variants_to_vcf script
    @drpatelh
    drpatelh authored Apr 14, 2022
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Commits on Apr 19, 2022

  1. added fasta arg and contig field to vcf header

    @saramonzon
    saramonzon committed Apr 19, 2022
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  2. fixed filter field

    @saramonzon
    saramonzon committed Apr 19, 2022
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  3. installed bcftools sort module

    @saramonzon
    saramonzon committed Apr 19, 2022
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  4. added bcftools sort step in ivar_variants subworkflow

    @saramonzon
    saramonzon committed Apr 19, 2022
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  5. removed sorting with awk in ivar_variants_to_vcf module

    @saramonzon
    saramonzon committed Apr 19, 2022
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  6. fixed import paths in modules

    @saramonzon
    saramonzon committed Apr 19, 2022
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  7. add fasta as input for ivar_variants_to_vcf module

    @saramonzon
    saramonzon committed Apr 19, 2022
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  8. black lint

    @saramonzon
    saramonzon committed Apr 19, 2022
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Commits on Apr 22, 2022

  1. updated mulled container for ivar_variants_to_vcf module

    @saramonzon
    saramonzon committed Apr 22, 2022
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  2. fixed bcftools sort in variants_ivar subworkflow and config

    @saramonzon
    saramonzon committed Apr 22, 2022
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Commits on Apr 25, 2022

  1. Replace vanilla Linux Biocontainer with Ubuntu

    @drpatelh
    drpatelh committed Apr 25, 2022
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  2. Replace vanilla Linux Biocontainer with Ubuntu

    @drpatelh
    drpatelh committed Apr 25, 2022
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  3. Merge pull request #307 from drpatelh/sync 

    Replace vanilla Linux Biocontainer with Ubuntu
    @drpatelh
    drpatelh authored Apr 25, 2022
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Commits on Apr 26, 2022

  1. Merge branch 'nf-core:dev' into dev

    @saramonzon
    saramonzon authored Apr 26, 2022
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  2. Updated changelog

    @saramonzon
    saramonzon committed Apr 26, 2022
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  3. prettier lint modules.json

    @saramonzon
    saramonzon committed Apr 26, 2022
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Commits on May 16, 2022

  1. Template update for nf-core/tools version 2.4

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    nf-core-bot committed May 16, 2022
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Commits on May 17, 2022

  1. Fix merge conflicts

    @drpatelh
    drpatelh committed May 17, 2022
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Commits on Jun 4, 2022

  1. Merge branch 'dev' into dev

    @saramonzon
    saramonzon authored Jun 4, 2022
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Commits on Jul 7, 2022

  1. Merge pull request #308 from BU-ISCIII/dev 

    Added contig tag to vcf in ivar_variants_to_vcf and included bcftools sort for vcf sorting
    @drpatelh
    drpatelh authored Jul 7, 2022
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  2. Follow up fix for PR #308

    @drpatelh
    drpatelh committed Jul 7, 2022
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  3. Run nf-core modules update

    @drpatelh
    drpatelh committed Jul 7, 2022
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  4. Intentionally ignore expected nf-core warnings

    @drpatelh
    drpatelh committed Jul 7, 2022
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  5. Re-install nf-core modules after updating tool versions

    @drpatelh
    drpatelh committed Jul 7, 2022
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  6. Re-install nf-core modules after updating tool versions

    @drpatelh
    drpatelh committed Jul 7, 2022
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Commits on Jul 8, 2022

  1. Fix tests after updating tool versions for all modules

    @drpatelh
    drpatelh committed Jul 8, 2022
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  2. Revert version bumps for SnpEff and SnpSift

    @drpatelh
    drpatelh committed Jul 8, 2022
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  3. Fix incorrect container definitions for SnpEff and SnpSift

    @drpatelh
    drpatelh committed Jul 8, 2022
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  4. Fix ECLint

    @drpatelh
    drpatelh committed Jul 8, 2022
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  5. Fix #292

    @drpatelh
    drpatelh committed Jul 8, 2022
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  6. Fix #292 again

    @drpatelh
    drpatelh committed Jul 8, 2022
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Commits on Jul 11, 2022

  1. Fix config bug - see issue 1722 on MultiQC repo

    @drpatelh
    drpatelh committed Jul 11, 2022
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  2. Add print statement back into ivar_variants_to_vcf.py scrip

    @drpatelh
    drpatelh committed Jul 11, 2022
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  3. Fix Pangolin and Nextclade lineage parsing issues

    @drpatelh
    drpatelh committed Jul 11, 2022
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  4. Fix publishDir bug introduced in PR 308

    @drpatelh
    drpatelh committed Jul 11, 2022
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  5. Fix #311

    @drpatelh
    drpatelh committed Jul 11, 2022
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  6. Fix #234

    @drpatelh
    drpatelh committed Jul 11, 2022
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  7. Bump pipeline version to 2.5

    @drpatelh
    drpatelh committed Jul 11, 2022
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  8. Fix publishing config relative to v2.4.1

    @drpatelh
    drpatelh committed Jul 11, 2022
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  9. Update CHANGELOG

    @drpatelh
    drpatelh committed Jul 11, 2022
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Commits on Jul 12, 2022

  1. Add manual version definition for artic modules

    @drpatelh
    drpatelh committed Jul 12, 2022
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  2. Update docs to update default Nextclade version being used

    @drpatelh
    drpatelh committed Jul 12, 2022
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  3. Merge pull request #314 from drpatelh/sync 

    Update modules and fix bugs for v2.5 release
    @drpatelh
    drpatelh authored Jul 12, 2022
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Commits on Jul 13, 2022

  1. Fix #316

    @drpatelh
    drpatelh committed Jul 13, 2022
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  2. Merge pull request #318 from drpatelh/sync 

    Fix #316
    @drpatelh
    drpatelh authored Jul 13, 2022
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