Hi all đź‘‹
Following advice from
@Phil Ewels, I’ve added
MultiQC custom content across my lightweight, teaching-friendly pipelines:
•
R1 Variant Splitter (R1 FASTQ → SNV/INDEL VCF split)
– emits ``*_mqc.tsv``; MultiQC auto-renders a section with SNV/INDEL counts per sample + one-click HTML
Repo:
https://github.com/samson-olofinsae/r1_batch_variant_pipeline
•
R2 QC Troubleshooter (Trimmomatic)
– CSV-backed custom table of pairing/trim stats; standalone builder + optional HTML
Repo:
https://github.com/samson-olofinsae/r2_qc_troubleshooter_pipeline
•
VCF QC (bcftools)
– custom table with PASS rate, Ti/Tv, het/hom, med DP/QUAL, multi-allelic %, etc. (+ General Stats)
Repo:
https://github.com/samson-olofinsae/vcf_qc_pipeline
Goal: make training runs reproducible, fault-tolerant, and at-a-glance via MultiQC.
Feedback welcome - especially on custom-content IDs/naming to align with MultiQC “house style”. Happy to PR examples if useful. 🙌