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Merging template updates 2.1 #56

Merged
merged 74 commits into from
Aug 25, 2021
Merged

Merging template updates 2.1 #56

merged 74 commits into from
Aug 25, 2021

Commits on Nov 19, 2020

  1. Template update for nf-core/tools version 1.12

    @nf-core-bot
    nf-core-bot committed Nov 19, 2020
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Commits on Dec 3, 2020

  1. Template update for nf-core/tools version 1.12.1

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    nf-core-bot committed Dec 3, 2020
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Commits on Mar 18, 2021

  1. Template update for nf-core/tools version 1.13

    @nf-core-bot
    nf-core-bot committed Mar 18, 2021
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Commits on Mar 19, 2021

  1. Template update for nf-core/tools version 1.13.1

    @nf-core-bot
    nf-core-bot committed Mar 19, 2021
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Commits on Mar 23, 2021

  1. Template update for nf-core/tools version 1.13.2

    @nf-core-bot
    nf-core-bot committed Mar 23, 2021
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Commits on Mar 25, 2021

  1. Template update for nf-core/tools version 1.13.3

    @nf-core-bot
    nf-core-bot committed Mar 25, 2021
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Commits on May 11, 2021

  1. Template update for nf-core/tools version 1.14

    @nf-core-bot
    nf-core-bot committed May 11, 2021
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Commits on Jul 13, 2021

  1. Template update for nf-core/tools version 2.0

    @KevinMenden
    KevinMenden committed Jul 13, 2021
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  2. Template update for nf-core/tools version 2.0.1

    @nf-core-bot
    nf-core-bot committed Jul 13, 2021
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Commits on Jul 27, 2021

  1. Template update for nf-core/tools version 2.1

    @nf-core-bot
    nf-core-bot committed Jul 27, 2021
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Commits on Aug 2, 2021

  1. barebone template update 2.1

    @d4straub
    d4straub committed Aug 2, 2021
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  2. fix CHANGELOG.md

    @d4straub
    d4straub committed Aug 2, 2021
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  3. fix linting

    @d4straub
    d4straub committed Aug 2, 2021
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  4. update description and README

    @d4straub
    d4straub committed Aug 2, 2021
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Commits on Aug 3, 2021

  1. update schema and version

    @d4straub
    d4straub committed Aug 3, 2021
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  2. change samplesheet to csv and fix parsing

    @d4straub
    d4straub committed Aug 3, 2021
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  3. fix linting

    @d4straub
    d4straub committed Aug 3, 2021
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  4. add skewer

    @d4straub
    d4straub committed Aug 3, 2021
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  5. fix linting

    @d4straub
    d4straub committed Aug 3, 2021
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Commits on Aug 4, 2021

  1. add more modules

    @d4straub
    d4straub committed Aug 4, 2021
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Commits on Aug 5, 2021

  1. from samplesheet csv to unicycler channels all fine

    @d4straub
    d4straub committed Aug 5, 2021
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Commits on Aug 6, 2021

  1. add skewer version

    @d4straub
    d4straub committed Aug 6, 2021
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  2. add prokka, kraken2 and quast

    @d4straub
    d4straub committed Aug 6, 2021
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  3. fix linting

    @d4straub
    d4straub committed Aug 6, 2021
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  4. samplesheet from tsv to csv again

    @d4straub
    d4straub committed Aug 6, 2021
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  5. use nf-core prokka module

    @d4straub
    d4straub committed Aug 6, 2021
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  6. add dfast

    @d4straub
    d4straub committed Aug 6, 2021
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Commits on Aug 9, 2021

  1. modify test profiles

    @d4straub
    d4straub committed Aug 9, 2021
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  2. create assembly channel

    @d4straub
    d4straub committed Aug 9, 2021
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  3. fix test_long_miniasm

    @d4straub
    d4straub committed Aug 9, 2021
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  4. add canu but test fails because reads do not overlap

    @d4straub
    d4straub committed Aug 9, 2021
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  5. add miniasm assembly

    @d4straub
    d4straub committed Aug 9, 2021
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  6. canu test_long: bacass_long_miniasm.csv instead bacass_long.csv

    @d4straub
    d4straub committed Aug 9, 2021
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  7. add consensus (racon) for miniasm

    @d4straub
    d4straub committed Aug 9, 2021
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  8. fix racon version output

    @d4straub
    d4straub committed Aug 9, 2021
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Commits on Aug 13, 2021

  1. fix test_long

    @d4straub
    d4straub committed Aug 13, 2021
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  2. add medaka

    @d4straub
    d4straub committed Aug 13, 2021
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Commits on Aug 16, 2021

  1. add nanopolish

    @d4straub
    d4straub committed Aug 16, 2021
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  2. adjust resources

    @d4straub
    d4straub committed Aug 16, 2021
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  3. fix test_long_miniasm

    @d4straub
    d4straub committed Aug 16, 2021
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  4. activate medaka for test_long_miniasm

    @d4straub
    d4straub committed Aug 16, 2021
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Commits on Aug 17, 2021

  1. fix miniasm assembly

    @d4straub
    d4straub committed Aug 17, 2021
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  2. fix kraken2 and activate for test_long_miniasm

    @d4straub
    d4straub committed Aug 17, 2021
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  3. adjust output folders

    @d4straub
    d4straub committed Aug 17, 2021
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Commits on Aug 18, 2021

  1. update CHANGELOG

    @d4straub
    d4straub committed Aug 18, 2021
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  2. fix kraken2 input

    @d4straub
    d4straub committed Aug 18, 2021
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  3. fix kraken2 output

    @d4straub
    d4straub committed Aug 18, 2021
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  4. fix kraken2 output 2

    @d4straub
    d4straub committed Aug 18, 2021
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  5. fix linting

    @d4straub
    d4straub committed Aug 18, 2021
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  6. refine output folders

    @d4straub
    d4straub committed Aug 18, 2021
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Commits on Aug 19, 2021

  1. add change in --krakendb

    @d4straub
    d4straub committed Aug 19, 2021
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  2. add zenodo doi

    @d4straub
    d4straub committed Aug 19, 2021
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  3. change dfast output to folder DFAST

    @d4straub
    d4straub committed Aug 19, 2021
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  4. update CITATTIONS

    @d4straub
    d4straub committed Aug 19, 2021
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  5. update README

    @d4straub
    d4straub committed Aug 19, 2021
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  6. update output docs

    @d4straub
    d4straub committed Aug 19, 2021
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  7. remove TODO

    @d4straub
    d4straub committed Aug 19, 2021
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  8. fix dfast

    @d4straub
    d4straub committed Aug 19, 2021
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  9. fix picoqc

    @d4straub
    d4straub committed Aug 19, 2021
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  10. fix linting and pycoqc

    @d4straub
    d4straub committed Aug 19, 2021
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  11. update output with medaka and nanopolish

    @d4straub
    d4straub committed Aug 19, 2021
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  12. remove samtools files from results folder

    @d4straub
    d4straub committed Aug 19, 2021
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  13. update parameter descriptions

    @d4straub
    d4straub committed Aug 19, 2021
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Commits on Aug 20, 2021

  1. remove parallel from nanopolish

    @d4straub
    d4straub committed Aug 20, 2021
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  2. fix pycoqc

    @d4straub
    d4straub committed Aug 20, 2021
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  3. amend output and update usage

    @d4straub
    d4straub committed Aug 20, 2021
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  4. remove tabs

    @d4straub
    d4straub committed Aug 20, 2021
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  5. fix nanopolish input

    @d4straub
    d4straub committed Aug 20, 2021
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  6. fix nanopolish input

    @d4straub
    d4straub committed Aug 20, 2021
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  7. remove unused samplesheet check and solve some TODOs

    @d4straub
    d4straub committed Aug 20, 2021
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Commits on Aug 23, 2021

  1. remove any connection to igenomes

    @d4straub
    d4straub committed Aug 23, 2021
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  2. add full size test dataset

    @d4straub
    d4straub committed Aug 23, 2021
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  3. removed unused parameter from test_long

    @d4straub
    d4straub committed Aug 23, 2021
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  4. ignore igenomes_base to avoid frequent warning with institutional pro… 

    …files
    @d4straub
    d4straub committed Aug 23, 2021
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