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wfi rewrite v0.4.0 #19

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7 of 11 tasks
ammaraziz opened this issue Dec 28, 2023 · 0 comments
Open
7 of 11 tasks

wfi rewrite v0.4.0 #19

ammaraziz opened this issue Dec 28, 2023 · 0 comments

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@ammaraziz
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ammaraziz commented Dec 28, 2023 •
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  • FIRST Rewrite and restructure snakefile into separate files: common.snk, paired.snk, single.snk, long.snk
  • Update ammaraziz::IRMA to latest version
  • Update rsv irma using the latest data
  • Incorporate nextclade for influenza, rsv, sc2
  • Replace cutadapt with fastp
  • add pTrimmer for trimming amplicon
  • Remove tiled related rules
  • Replace R code with python/toyplot specific code
  • Add depth masking option
  • Incorporate snaketools for CLI usage #21
  • Add csv file as input - use prepare.py
ammaraziz added a commit that referenced this issue Feb 8, 2024
@ammaraziz
added prepare.py to irmakit.py #19
0eecd1d
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