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chore: release 1.0.1 #70

Merged
merged 41 commits into from
Sep 11, 2024
Merged

chore: release 1.0.1 #70

merged 41 commits into from
Sep 11, 2024

Commits on May 23, 2024

  1. updates post 1.0.0 release

    @nh13
    nh13 committed May 23, 2024
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Commits on May 24, 2024

  1. Update README.md

    @nh13
    nh13 authored May 24, 2024
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Commits on May 25, 2024

  1. ci: fix nf-test fastquorum versions for v1.0.1

    @nh13
    nh13 committed May 25, 2024
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Commits on May 27, 2024

  1. Apply suggestions from code review 

    Co-authored-by: Maxime U Garcia <[email protected]>
    @nh13 @maxulysse
    nh13 and maxulysse authored May 27, 2024
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Commits on May 30, 2024

  1. docs: update subway diagrams 

    Fixes a bug where alignment and filtering where swapped in the phase 2
high-throughput diagrams.  Thanks James Fellows Yates (@jfy133)
    @nh13
    nh13 committed May 30, 2024
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  2. update CHANGELOG for #51

    @nh13
    nh13 committed May 30, 2024
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Commits on Jun 5, 2024

  1. Add when conditions to prepare genome so they only run if not given

    @SPPearce
    SPPearce committed Jun 5, 2024
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  2. Merge remote-tracking branch 'origin/dev' into prepare_genome_when

    @SPPearce
    SPPearce committed Jun 5, 2024
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  3. Update Changelog

    @SPPearce
    SPPearce committed Jun 5, 2024
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  4. Merge branch 'dev' into dev-post-1.0.0

    @SPPearce
    SPPearce authored Jun 5, 2024
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Commits on Jul 15, 2024

  1. Merge pull request #50 from nf-core/dev-post-1.0.0 

    updates post 1.0.0 release
    @nh13
    nh13 authored Jul 15, 2024
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  2. Move filterconsensusreads memory to base.config

    @SPPearce
    SPPearce committed Jul 15, 2024
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  3. Merge remote-tracking branch 'origin/dev' into sppearce/hardcoded-gb-… 

    …limit-in-57
    @SPPearce
    SPPearce committed Jul 15, 2024
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  4. Update Changelog

    @SPPearce
    SPPearce committed Jul 15, 2024
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Commits on Jul 17, 2024

  1. Merge pull request #58 from nf-core/prepare_genome_when 

    Add when conditions to prepare
    @nh13
    nh13 authored Jul 17, 2024
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  2. Merge branch 'dev' into sppearce/hardcoded-gb-limit-in-57

    @SPPearce
    SPPearce authored Jul 17, 2024
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Commits on Jul 18, 2024

  1. Move process resource requests into modules.config

    @SPPearce
    SPPearce committed Jul 18, 2024
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Commits on Jul 19, 2024

  1. Merge pull request #60 from nf-core/sppearce/hardcoded-gb-limit-in-57 

    Allow escalation of memory for FilterConsensusReads
    @SPPearce
    SPPearce authored Jul 19, 2024
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  2. Allow igenomes to set params

    @SPPearce
    SPPearce committed Jul 19, 2024
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  3. fix: support when multiple value args can be a number or a 

    comma-delimited string

Fixes #62
    @nh13
    nh13 committed Jul 19, 2024
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Commits on Jul 22, 2024

  1. Remove uncalled checkPathParamList

    @SPPearce
    SPPearce committed Jul 22, 2024
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  2. Update CHANGELOG and schema

    @SPPearce
    SPPearce committed Jul 22, 2024
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Commits on Aug 1, 2024

  1. Update nextflow.config 

    Co-authored-by: Nils Homer <[email protected]>
    @SPPearce @nh13
    SPPearce and nh13 authored Aug 1, 2024
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Commits on Aug 2, 2024

  1. bugfix: merging lanes would result in an error 

    There's a bug in `samtools merge --template-coordinate' that causes
the output not to be correctly sorted.  Here, we re-sort via fgbio
SortBam to ensure the output is properly sorted.

fgbio SortBam can be removed when the fix to the samtools bug is
released.

See:
samtools/samtools#2062
    @nh13
    nh13 committed Aug 2, 2024
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  2. Apply suggestions from code review 

    Co-authored-by: Simon Pearce <[email protected]>
    @nh13 @SPPearce
    nh13 and SPPearce committed Aug 2, 2024
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  3. Merge pull request #67 from nf-core/igenomes_fix 

    Allow igenomes to work
    @SPPearce
    SPPearce authored Aug 2, 2024
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Commits on Aug 22, 2024

  1. chore: update module versions

    @znorgaard
    znorgaard committed Aug 22, 2024
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  2. chore: update changelog

    @znorgaard
    znorgaard committed Aug 22, 2024
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  3. chore: update version

    @znorgaard
    znorgaard committed Aug 22, 2024
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  4. chore: add contributors

    @znorgaard
    znorgaard committed Aug 22, 2024
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Commits on Aug 23, 2024

  1. fix: downgrade multiqc

    @znorgaard
    znorgaard committed Aug 23, 2024
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  2. chore: update multiqc module

    @znorgaard
    znorgaard committed Aug 23, 2024
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  3. chore: update subworkflow

    @znorgaard
    znorgaard committed Aug 23, 2024
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  4. chore: update snapshots

    @znorgaard
    znorgaard committed Aug 23, 2024
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Commits on Sep 4, 2024

  1. chore: finalize release date

    @znorgaard
    znorgaard committed Sep 4, 2024
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  2. Merge pull request #69 from nf-core/zn_release 

    chore: prepare for 1.0.1 release
    @znorgaard
    znorgaard authored Sep 4, 2024
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Commits on Sep 5, 2024

  1. Add stubs to all modules

    @SPPearce
    SPPearce committed Sep 5, 2024
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  2. Update modules/local/fgbio/collectduplexseqmetrics/main.nf

    @SPPearce
    SPPearce authored Sep 5, 2024
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Commits on Sep 6, 2024

  1. Merge pull request #71 from nf-core/add_stub 

    Add stubs to all local modules
    @SPPearce
    SPPearce authored Sep 6, 2024
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Commits on Sep 10, 2024

  1. chore: correct date

    @znorgaard
    znorgaard committed Sep 10, 2024
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  2. Merge pull request #75 from nf-core/zn_readme_date 

    chore: correct date
    @znorgaard
    znorgaard authored Sep 10, 2024
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