December 18, 2025
‘Tis the season for failed pipelines, missing samples, and Slack messages at 9 PM. 🎄
If you’ve ever been the computational team at a scaling biotech company, you know exactly what I’m talking about. Here’s my holiday gift to everyone who’s debugged a pipeline on Christmas Eve:
🧬 The Twelve Days of Scale-Up
On the first day of scale-up, the wet lab gave to me:
A pipeline running on Batch
On the second day of scale-up, the wet lab gave to me:
Two FASTQ files
And a pipeline running on Batch
On the third day of scale-up, the wet lab gave to me:
Three QC checks
Two FASTQ files
And a pipeline running on Batch
On the fourth day of scale-up, the wet lab gave to me:
Four missing samples
Three QC checks
Two FASTQ files
And a pipeline running on Batch
On the fifth day of scale-up, the wet lab gave to me:
FIVE FAILED RUNS
Four missing samples
Three QC checks
Two FASTQ files
And a pipeline running on Batch
On the sixth day of scale-up, the wet lab gave to me:
Six adapters trimming
FIVE FAILED RUNS
Four missing samples
Three QC checks
Two FASTQ files
And a pipeline running on Batch
On the seventh day of scale-up, the wet lab gave to me:
Seven contigs mapping
Six adapters trimming
FIVE FAILED RUNS
Four missing samples
Three QC checks
Two FASTQ files
And a pipeline running on Batch
On the eighth day of scale-up, the wet lab gave to me:
Eight BAMs a-sorting
Seven contigs mapping
Six adapters trimming
FIVE FAILED RUNS
Four missing samples
Three QC checks
Two FASTQ files
And a pipeline running on Batch
On the ninth day of scale-up, the wet lab gave to me:
Nine VCFs a-calling
Eight BAMs a-sorting
Seven contigs mapping
Six adapters trimming
FIVE FAILED RUNS
Four missing samples
Three QC checks
Two FASTQ files
And a pipeline running on Batch
On the tenth day of scale-up, the wet lab gave to me:
Ten Slacks a-pinging
Nine VCFs a-calling
Eight BAMs a-sorting
Seven contigs mapping
Six adapters trimming
FIVE FAILED RUNS
Four missing samples
Three QC checks
Two FASTQ files
And a pipeline running on Batch
On the eleventh day of scale-up, the wet lab gave to me:
Eleven p-vals adjusting
Ten Slacks a-pinging
Nine VCFs a-calling
Eight BAMs a-sorting
Seven contigs mapping
Six adapters trimming
FIVE FAILED RUNS
Four missing samples
Three QC checks
Two FASTQ files
And a pipeline running on Batch
On the twelfth day of scale-up, the wet lab gave to me:
Twelve figures plotting
Eleven p-vals adjusting
Ten Slacks a-pinging
Nine VCFs a-calling
Eight BAMs a-sorting
Seven contigs mapping
Six adapters trimming
FIVE FAILED RUNS
Four missing samples
Three QC checks
Two FASTQ files
And a pipeline running on Batch
May your pipelines run smoothly and your endpoints be significant this holiday season. 🎵
What’s your most memorable “holiday debugging” story?
