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Patch release 2.4.5 #911

Merged
merged 90 commits into from
Aug 2, 2022
Merged

Patch release 2.4.5 #911

merged 90 commits into from
Aug 2, 2022

Commits on Sep 6, 2021

  1. Switch hostremoval_input_fastq from multiprocessing to multithreading… 

    … because of memory concerns
    @maxibor
    maxibor committed Sep 6, 2021
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Commits on Sep 7, 2021

  1. switch fastq parsing to pysam

    @maxibor
    maxibor committed Sep 7, 2021
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  2. update log message

    @maxibor
    maxibor committed Sep 7, 2021
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Commits on Oct 12, 2021

  1. speed and memory optimization

    @maxibor
    maxibor committed Oct 12, 2021
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  2. merge from upstream

    @maxibor
    maxibor committed Oct 12, 2021
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  3. update changelog

    @maxibor
    maxibor committed Oct 12, 2021
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  4. add missing return character

    @maxibor
    maxibor committed Oct 12, 2021
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Commits on Apr 25, 2022

  1. define DSL1 explicitly, as Nextflow made DSL2 default 

    Signed-off-by: Lehmann_Fabian <[email protected]>
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    Lehmann-Fabian committed Apr 25, 2022
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Commits on Apr 26, 2022

  1. Added information to Changelog.md 

    Signed-off-by: Lehmann_Fabian <[email protected]>
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    Lehmann-Fabian committed Apr 26, 2022
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  2. Update CHANGELOG.md

    @jfy133
    jfy133 authored Apr 26, 2022
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  3. Update CHANGELOG.md

    @jfy133
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  4. Merge pull request #882 from Lehmann-Fabian/dev 

    Define DSL1 explicitly, as Nextflow made DSL2 default
    @jfy133
    jfy133 authored Apr 26, 2022
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  5. Fix raw FASTQC single-end threads

    @jfy133
    jfy133 authored Apr 26, 2022
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  6. Update CHANGELOG.md

    @jfy133
    jfy133 authored Apr 26, 2022
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  7. Update CHANGELOG.md

    @jfy133
    jfy133 authored Apr 26, 2022
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Commits on Apr 29, 2022

  1. move fastq to pysam

    @maxibor
    maxibor committed Apr 29, 2022
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  2. Merge branch 'dev' of github.com:maxibor/eager into dev

    @maxibor
    maxibor committed Apr 29, 2022
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Commits on May 5, 2022

  1. Merge pull request #883 from nf-core/fastqc-thread-fix 

    Fastqc thread fix
    @jfy133
    jfy133 authored May 5, 2022
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Commits on May 23, 2022

  1. fix host_removal flags

    @maxibor
    maxibor committed May 23, 2022
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Commits on May 30, 2022

  1. Add memory to all java tools in get_software_versions

    @jfy133
    jfy133 committed May 30, 2022
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  2. Phrasing Tweak

    @jfy133
    jfy133 committed May 30, 2022
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  3. Fix issue number in link

    @jfy133
    jfy133 committed May 30, 2022
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  4. Clarify clip_readlength help text for what is considered ultra-short … 

    …reads
    @jfy133
    jfy133 committed May 30, 2022
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  5. Remove deprecated params from benchmarking profiles

    @jfy133
    jfy133 committed May 30, 2022
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Commits on Jun 2, 2022

  1. Changelog

    @jfy133
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Commits on Jun 3, 2022

  1. Relace bbduk version with bbversion.sh

    @jfy133
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Commits on Jun 13, 2022

  1. Typo fix and location output docs in pipeline summary

    @jfy133
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Commits on Jul 1, 2022

  1. Allow no output from Kraken2 e.g. for negative controls with no reads

    @jfy133
    jfy133 authored Jul 1, 2022
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  2. Update CHANGELOG.md

    @jfy133
    jfy133 authored Jul 1, 2022
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Commits on Jul 4, 2022

  1. Merge pull request #890 from nf-core/patch-getsoftwraeversions-java 

    Patch getsoftwareversions java tools
    @jfy133
    jfy133 authored Jul 4, 2022
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  2. Merge branch 'dev' into patch-improve_clipreadlength_desc

    @jfy133
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  3. Update CHANGELOG.md 

    Co-authored-by: Thiseas C. Lamnidis <[email protected]>
    @jfy133 @TCLamnidis
    jfy133 and TCLamnidis authored Jul 4, 2022
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  4. Merge branch 'dev' into patch-testconfig_params_updates

    @jfy133
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  5. Merge branch 'dev' into output-docs-improvements

    @jfy133
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  6. Merge branch 'dev' into kraken2-emptyfastq-fix

    @jfy133
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  7. Merge pull request #891 from nf-core/patch-improve_clipreadlength_desc 

    Clarify clip_readlength help text for what is considered ultra-short …
    @jfy133
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  8. Merge branch 'dev' into patch-testconfig_params_updates

    @jfy133
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  9. Merge pull request #892 from nf-core/patch-testconfig_params_updates 

    Remove deprecated params from benchmarking profiles
    @jfy133
    jfy133 authored Jul 4, 2022
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  10. Merge branch 'dev' into output-docs-improvements

    @jfy133
    jfy133 authored Jul 4, 2022
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  11. Merge pull request #896 from nf-core/output-docs-improvements 

    Output docs improvements
    @jfy133
    jfy133 authored Jul 4, 2022
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  12. Merge branch 'dev' into kraken2-emptyfastq-fix

    @jfy133
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Commits on Jul 8, 2022

  1. Update output.md

    @jfy133
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  2. Merge pull request #898 from nf-core/kraken2-emptyfastq-fix 

    Kraken2 empty fastq resulting in no output file fix
    @jfy133
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Commits on Jul 12, 2022

  1. Fix circulargenerator assuming .fasta extension

    @jfy133
    jfy133 committed Jul 12, 2022
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  2. Add .gitpod.yml for remote working

    @jfy133
    jfy133 authored Jul 12, 2022
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  3. Merge pull request #901 from nf-core/gitpod 

    Add .gitpod.yml for remote working
    @jfy133
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Commits on Jul 13, 2022

  1. Merge pull request #900 from nf-core/circularmapper-fix 

    Fix circulargenerator assuming .fasta extension
    @jfy133
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Commits on Jul 16, 2022

  1. Remove old dumps

    @jfy133
    jfy133 committed Jul 16, 2022
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  2. Fix failed of endorspy to execute or cache on resume

    @jfy133
    jfy133 committed Jul 16, 2022
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  3. Grammar

    @jfy133
    jfy133 committed Jul 16, 2022
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  4. Remove unused code

    @jfy133
    jfy133 committed Jul 16, 2022
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  5. Undo more debugging

    @jfy133
    jfy133 committed Jul 16, 2022
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  6. Fix missing defaults

    @jfy133
    jfy133 committed Jul 16, 2022
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  7. Update changelgo

    @jfy133
    jfy133 committed Jul 16, 2022
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Commits on Jul 18, 2022

  1. Merge pull request #903 from nf-core/defaults-fix 

    Defaults fix
    @jfy133
    jfy133 authored Jul 18, 2022
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Commits on Jul 20, 2022

  1. Merge remote-tracking branch 'upstream/dev' into dev

    @maxibor
    maxibor committed Jul 20, 2022
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  2. threads is proc

    @maxibor
    maxibor committed Jul 20, 2022
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  3. remove return set

    @maxibor
    maxibor committed Jul 20, 2022
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  4. update changelog

    @maxibor
    maxibor committed Jul 20, 2022
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  5. Update CHANGELOG.md

    @jfy133
    jfy133 authored Jul 20, 2022
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  6. Bump MultiQC so we get proper AR2 plots

    @jfy133
    jfy133 committed Jul 20, 2022
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Commits on Jul 21, 2022

  1. Merge pull request #907 from nf-core/multiqc-update 

    Bump MultiQC so we get proper AR2 plots
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Commits on Jul 25, 2022

  1. Minor modification

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Commits on Jul 26, 2022

  1. Merge pull request #905 from maxibor/dev 

    Speed and memory optimization of `extract_map_reads.py`
    @jfy133
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Commits on Jul 27, 2022

  1. Merge pull request #908 from nf-core/tube-update 

    Minor update tube update
    @jfy133
    jfy133 authored Jul 27, 2022
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  2. Add path call in pileupcaller bams

    @TCLamnidis
    TCLamnidis authored Jul 27, 2022
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Commits on Jul 28, 2022

  1. fix pileupcaller path input. paths in bamtrim.

    @TCLamnidis
    TCLamnidis committed Jul 28, 2022
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  2. Update CHANGELOG.md

    @TCLamnidis
    TCLamnidis committed Jul 28, 2022
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Commits on Jul 29, 2022

  1. Pin to later version of node as in nf-core/tools#1398

    @jfy133
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  2. Update linting.yml

    @jfy133
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  3. Update .nf-core-lint.yml

    @jfy133
    jfy133 authored Jul 29, 2022
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  4. prettier fixes

    @jfy133
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  5. Fix markdown linting

    @jfy133
    jfy133 committed Jul 29, 2022
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  6. Revert nf-core non-standard linting files but still template

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  7. Revert "Revert nf-core non-standard linting files but still template" 

    This reverts commit f5f805c.
    @jfy133
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  8. Revert "Fix markdown linting" 

    This reverts commit f6ebee3.
    @jfy133
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  9. Revert "prettier fixes" 

    This reverts commit 99046cb.
    @jfy133
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  10. Fix markdown linting

    @jfy133
    jfy133 committed Jul 29, 2022
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  11. Merge pull request #909 from nf-core/pileupcaller_paths_fix 

    Pileupcaller paths fix
    @jfy133
    jfy133 authored Jul 29, 2022
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  12. Final markdown linting

    @jfy133
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  13. Fix inconssitency with template

    @jfy133
    jfy133 committed Jul 29, 2022
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  14. Missing new line

    @jfy133
    jfy133 committed Jul 29, 2022
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  15. Try custom yaml linting

    @jfy133
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  16. fix yaml lint config param

    @jfy133
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  17. Merge pull request #910 from nf-core/linting-fixes 

    Linting fixes
    @jfy133
    jfy133 authored Jul 29, 2022
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  18. Merge branch 'dev' into endorspy-resume-fix

    @jfy133
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  19. Merge pull request #902 from nf-core/endorspy-resume-fix 

    Endorspy resume fix
    @jfy133
    jfy133 authored Jul 29, 2022
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  20. Bump versions for release

    @jfy133
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Commits on Jul 31, 2022

  1. Apply suggestions from code review

    @jfy133
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Commits on Aug 2, 2022

  1. Apply suggestions from code review 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
    @TCLamnidis @mashehu
    TCLamnidis and mashehu authored Aug 2, 2022
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