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Ribodetector and RustQC Additions#47

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mikemartinez99 wants to merge 11 commits into
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Ribodetector and RustQC Additions#47
mikemartinez99 wants to merge 11 commits into
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dev-ribodetector

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@mikemartinez99 mikemartinez99 commented Apr 17, 2026 •
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Ribodetector

  • Implemented ribodetector rule in snakefile
  • Added scripts/ribo_stats.sh to generate ribs statistics compatible with MultiQC

RustQC

  • Added optional parameter to invoke RustQC, if false, samtools stats is ran as it previously was
  • Added singularity call instructions to job.script.sh if run_rustqc is true
  • Added rustqc rule to Snakefile
  • Dynamically generate multiqc report to include rustQC and ribodetector outputs depending on if they are invoked or not.
  • Tested outputs against previous pipeline run

General linting

  • Added messages to each Snakemake rule for easier log parsing
  • Added toggle params in config.yaml and all prebuilt_configs for ribodetector and rustQC

@mikemartinez99
Ribodetector and RustQC additions
a26ddda 
- Implemented ribodetector rules and associated conda environment
- Implemented RustQC and added singularity requirement in job script to run it.
- Updated multiqc config to support branding to CQB and new QC report
- IMplemented basic QC report (what we previously had) and detailed QC report
@mikemartinez99
Ribodetector params in prebuilt configs
695b049
@mikemartinez99 mikemartinez99 added the enhancement New feature or request label Apr 17, 2026
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@owenwilkins owenwilkins Awaiting requested review from owenwilkins

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@mikemartinez99 @brbergamo