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wfi-snakemake - version 0.3
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@ammaraziz ammaraziz released this 21 Oct 06:18
· 75 commits to master since this release
v0.3
a12abde
  • Summary reports are generated including text report and combined depth plot
  • Updated minimum depth cutoff for calling SNVs and indels (now 5% and 8% respectively)
  • Added new module for RSV organism
    • Note: RSV-secondary requires further testing
    • Note: minimap2 modules are present but not integrated in pipeline (planned for future releases)
  • Reworked pattern matching for sample names: {sample}_{lane}_{pair}_{run}.fastq.gz
  • Added option to change file pattern matching
  • Removed read trimming step completely - IRMA does read filtering and trimming internally
  • Added primer filtering with cutadapt for FLU and RSV
  • Added QC tables as part of the output
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