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release of ViralFlow version 1.0.0#40

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alexandrefreitasdasilva merged 41 commits intomaindezordi/ViralFlow:mainfrom developdezordi/ViralFlow:developCopy head branch name to clipboardNov 20, 2023

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Commits

Commits on Sep 23, 2023

• Vfnext docs (#28)

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Commits on Oct 9, 2023

• fix compileOutput.py script to run on viralflow env

  

  Alexandre Freitas

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Commits on Oct 11, 2023

• update env.yml

  

  Alexandre Freitas

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• fix snpeff error when running on HPC

  

  Alexandre Freitas

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• update of recipes to include procps to get nextflow metrics

  

  Alexandre Freitas

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Commits on Oct 12, 2023

• fix splitting of R1 and R2 unmapped reads

  alexandrefreitasdasilva

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Commits on Oct 13, 2023

• update of files to run intrahost on viralflow env

  

  Alexandre Freitas

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Commits on Oct 14, 2023

• adding bamdash tool for coverage plot generation

  

  Alexandre Freitas

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• update coveragePlot.nf

  

  Alexandre Freitas

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• update files

  

  Alexandre Freitas

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• update coveragePlot.nf to include png output

  

  Alexandre Freitas

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• Update setup.py

  dezordi

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• Update main.nf

  dezordi

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Commits on Oct 16, 2023

• Update vfnext/modules/getUnmappedReads.nf

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• Update vfnext/modules/getUnmappedReads.nf

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Commits on Oct 17, 2023

• update env.yml to include libs necessary to collect system metrics

  

  Alexandre Freitas

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Commits on Nov 3, 2023

• Merge pull request #29 from dezordi/develop_fixcompiled

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• Merge pull request #30 from dezordi/develop_fixNextflowMetrics

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• Merge pull request #31 from dezordi/develop_fixUnmappedreads

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• Merge pull request #32 from dezordi/fix_intahostScript

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• Merge pull request #33 from dezordi/develop_bamdashFeature

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Commits on Nov 6, 2023

• solving fixWGS to run on viralflow env

  alexandrefreitasdasilva

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Commits on Nov 9, 2023

• adding default reference genomes

  alexandrefreitasdasilva

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• Merge pull request #37 from dezordi/develop_fixwgs

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• update singularity to version 3.11.4; configs updated to use .sif file instead sandbox. PS: snpeff, pangolin and nextclade still in sandbox

  

  costahud

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• fix script on build env

  

  costahud

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• fixing scripts on building containers

  

  costahud

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• fixing script on pull container

  

  costahud

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Commits on Nov 12, 2023

• adding snpPlot module

  alexandrefreitasdasilva

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Commits on Nov 16, 2023

• changing nextclade sandbox to sif

  alexandrefreitasdasilva

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• adding parameter to force the pull containers

  alexandrefreitasdasilva

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Commits on Nov 17, 2023

• fix repositories_viral_flow.txt

  alexandrefreitasdasilva

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• adjusting build_containers.py

  alexandrefreitasdasilva

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Commits on Nov 18, 2023

• adjusting build_containers.py

  alexandrefreitasdasilva

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• cheanging version

  alexandrefreitasdasilva

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• adjusting build_containers.py

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• adjusting build_containers.py

  alexandrefreitasdasilva

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• Update build_containers.py

  alexandrefreitasdasilva

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Commits on Nov 19, 2023

• adjusting the release version and new tasks

  alexandrefreitasdasilva

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• adjusting tast.rst file

  alexandrefreitasdasilva

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• Merge pull request #39 from dezordi/develop_update_containers

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