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update dev with main #29

Merged
merged 103 commits into from
Jul 6, 2022
Merged

update dev with main #29

merged 103 commits into from
Jul 6, 2022

Commits on Oct 8, 2021

  1. Update LMAS.nf

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    cimendes authored Oct 8, 2021
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Commits on Oct 11, 2021

  1. add nextflow CI test

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    cimendes committed Oct 11, 2021
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  2. fix yml

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    cimendes committed Oct 11, 2021
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  3. Update ci_nextflow.yml

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    cimendes committed Oct 11, 2021
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  4. Update ci_nextflow.yml

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    cimendes committed Oct 11, 2021
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  5. Update ci_nextflow.yml

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    cimendes committed Oct 11, 2021
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  6. Update params.config

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    cimendes committed Oct 11, 2021
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  7. Update test.config

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    cimendes committed Oct 11, 2021
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  8. Update ci_nextflow.yml

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    cimendes committed Oct 11, 2021
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  9. add nextflow command ffor test

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    cimendes committed Oct 11, 2021
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  10. Update ci_nextflow.yml

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    cimendes committed Oct 11, 2021
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  11. fix memory and cpu params

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    cimendes committed Oct 11, 2021
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Commits on Oct 12, 2021

  1. try to add option to limit resources globally

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    cimendes committed Oct 12, 2021
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  2. Update nextflow.config

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    cimendes committed Oct 12, 2021
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  3. move resources to main config file

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    cimendes committed Oct 12, 2021
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  4. fix max_memory param

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    cimendes committed Oct 12, 2021
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  5. add missing labels

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    cimendes committed Oct 12, 2021
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  6. fix issues created by linter; update test data

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    cimendes committed Oct 12, 2021
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  7. Update .gitignore

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    cimendes committed Oct 12, 2021
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  8. run ci on main branch

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    cimendes committed Oct 12, 2021
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  9. up version

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    cimendes committed Oct 12, 2021
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  10. Create triple_reference.fasta

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    cimendes committed Oct 12, 2021
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  11. Merge pull request #16 from cimendes/dev-ci 

    Add CI to workflow
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    cimendes authored Oct 12, 2021
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  12. Update README.md

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    cimendes authored Oct 12, 2021
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Commits on Oct 14, 2021

  1. fix optional md

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    cimendes committed Oct 14, 2021
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  2. Update compile_reports.py

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    cimendes committed Oct 14, 2021
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  3. Update LMAS.nf

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    cimendes committed Oct 14, 2021
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  4. Update LMAS.nf

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    cimendes committed Oct 14, 2021
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  5. update message in report when md file is not provided

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    cimendes committed Oct 14, 2021
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  6. Update profiles.config

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    cimendes committed Oct 14, 2021
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  7. remove qos

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    cimendes committed Oct 14, 2021
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Commits on Oct 16, 2021

  1. mount basedir in docker containters; adjust results for single sample… 

    … with missing plots
    @cimendes
    cimendes committed Oct 16, 2021
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  2. bind basedir with singularity

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    cimendes committed Oct 16, 2021
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Commits on Oct 17, 2021

  1. Update nextflow.config

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    cimendes committed Oct 17, 2021
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Commits on Oct 19, 2021

  1. Update LMAS_ECCMID.png

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    cimendes committed Oct 19, 2021
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  2. Update nextflow.config

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    cimendes authored Oct 19, 2021
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  3. update help message

    @cimendes
    cimendes committed Oct 19, 2021
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  4. update README and script to download zymos data

    @cimendes
    cimendes committed Oct 19, 2021
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  5. update docs

    @cimendes
    cimendes committed Oct 19, 2021
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Commits on Oct 22, 2021

  1. Update main.js.zip

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    cimendes committed Oct 22, 2021
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  2. Merge pull request #17 from cimendes/main 

    update to main
    @cimendes
    cimendes authored Oct 22, 2021
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  3. Update README.md

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    cimendes committed Oct 22, 2021
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  4. dls2 conversion begins...

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    cimendes committed Oct 22, 2021
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  5. split processes into modules

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    cimendes committed Oct 22, 2021
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Commits on Oct 25, 2021

  1. Update README.md

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    cimendes authored Oct 25, 2021
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Commits on Oct 26, 2021

  1. Update metrics.rst

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    cimendes authored Oct 26, 2021
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Commits on Oct 27, 2021

  1. fix bug where secondary mappings were being reported by minimap2

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    cimendes committed Oct 27, 2021
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  2. fix typo

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    cimendes committed Oct 27, 2021
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Commits on Oct 28, 2021

  1. up version

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    cimendes committed Oct 28, 2021
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  2. Update LMAS.nf

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    cimendes committed Oct 28, 2021
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Commits on Oct 30, 2021

  1. Add missing assemblers to assembler names list

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    cimendes committed Oct 30, 2021
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Commits on Nov 22, 2021

  1. Update README.md

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    cimendes authored Nov 22, 2021
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  2. Update overview.rst

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    cimendes authored Nov 22, 2021
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  3. Update README.md

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    cimendes authored Nov 22, 2021
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Commits on Nov 23, 2021

  1. skip placeholder in table when assembly process is skipped

    @cimendes
    cimendes committed Nov 23, 2021
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  2. version bump to 1.1.3

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    cimendes committed Nov 23, 2021
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  3. Update LMAS.nf

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    cimendes committed Nov 23, 2021
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Commits on Nov 25, 2021

  1. Update LMAS_DIAGRAM_FULL.png

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    cimendes committed Nov 25, 2021
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Commits on Dec 2, 2021

  1. Merge branch 'main' into dev-dsl2

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    cimendes committed Dec 2, 2021
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  2. start conversion to dsl2 - better than expected!

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    cimendes committed Dec 2, 2021
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Commits on Dec 6, 2021

  1. Update README.md

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    cimendes authored Dec 6, 2021
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  2. add mapping workflow, add processes to produce results and final repo… 

    …rt. First draft conversion done
    @cimendes
    cimendes committed Dec 6, 2021
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  3. change module name

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    cimendes committed Dec 6, 2021
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  4. move compile report to separate file

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    cimendes committed Dec 6, 2021
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  5. move report to separate wf

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    cimendes committed Dec 6, 2021
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Commits on Dec 7, 2021

  1. move preprocessing to separate workflow

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    cimendes committed Dec 7, 2021
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  2. move postprocessing processes to a new module

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    cimendes committed Dec 7, 2021
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  3. add wrapper for calling LMAS workflow

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    cimendes committed Dec 7, 2021
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  4. add README to all modules

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    cimendes committed Dec 7, 2021
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  5. add eval command

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    cimendes committed Dec 7, 2021
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  6. Merge branch 'main' into dev-dsl2

    @cimendes
    cimendes authored Dec 7, 2021
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  7. fix process name in conf/containers.config; add check that workflow c… 

    …ompleted successfully by checking that report file exists
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    cimendes committed Dec 7, 2021
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  8. add feedback for successful run

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    cimendes committed Dec 7, 2021
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  9. Update README.md

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    cimendes committed Dec 7, 2021
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Commits on Dec 9, 2021

  1. update documentation for DSL2

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    cimendes committed Dec 9, 2021
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  2. Update basic_usage.rst

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    cimendes committed Dec 9, 2021
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Commits on Dec 10, 2021

  1. Merge pull request #18 from B-UMMI/dev-dsl2 

    LMAS 2.0.0: Update to DSL2
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    cimendes authored Dec 10, 2021
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Commits on Mar 25, 2022

  1. add version parameter and bump version

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    cimendes committed Mar 25, 2022
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Commits on Apr 6, 2022

  1. add conda badges

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    cimendes committed Apr 6, 2022
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  2. Update README.md

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    cimendes committed Apr 6, 2022
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  3. Update README.md

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    cimendes committed Apr 6, 2022
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  4. Update README.md

    @cimendes
    cimendes committed Apr 6, 2022
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  5. Update README.md

    @cimendes
    cimendes committed Apr 6, 2022
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  6. Update installation.rst

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Commits on Apr 7, 2022

  1. Merge pull request #20 from B-UMMI/update_docs 

    Update docs to include Bioconda installation option
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Commits on May 19, 2022

  1. Update README.md

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Commits on Jun 14, 2022

  1. update ci with singularity test

    @cimendes
    cimendes committed Jun 14, 2022
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  2. Update ci_nextflow.yml

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    cimendes committed Jun 14, 2022
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  3. Update profiles.config

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    cimendes committed Jun 14, 2022
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  4. Update ci_nextflow.yml

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    cimendes committed Jun 14, 2022
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  5. Merge pull request #23 from B-UMMI/update_ci 

    Update ci with singularity test
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Commits on Jun 28, 2022

  1. Update params.config

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  2. Merge pull request #24 from B-UMMI/change_defaults_assemblers 

    Change defaults on assembly parameters
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    cimendes authored Jun 28, 2022
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Commits on Jun 30, 2022

  1. remove BCALM2 from workflow

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    cimendes committed Jun 30, 2022
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Commits on Jul 1, 2022

  1. Merge pull request #25 from B-UMMI/remove_bcalm2 

    remove BCALM2 from workflow
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  2. Update main.nf

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    cimendes committed Jul 1, 2022
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  3. Merge pull request #26 from B-UMMI/remove_bcalm2 

    patch fix - Unknown method invocation
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Commits on Jul 4, 2022

  1. fix bug where gap and snp plots were not being computed for all assem… 

    …blers
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    cimendes committed Jul 4, 2022
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  2. remove mention of BCALM2 - deprecated from LMAS

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    cimendes committed Jul 4, 2022
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  3. Merge pull request #27 from B-UMMI/fix_gap_plot 

    [Patch fix] - Gap and SPN plots
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    cimendes authored Jul 4, 2022
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  4. Update LMAS_ECCMID.png

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    cimendes committed Jul 4, 2022
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Commits on Jul 6, 2022

  1. Fix bug - empty performance table

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    cimendes committed Jul 6, 2022
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  2. Merge pull request #28 from B-UMMI/fix_gap_plot 

    Fix bug - empty performance table
    @cimendes
    cimendes authored Jul 6, 2022
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