Recipes

Recipes

Short patterns for everyday jobs. Each keeps the exit status and output behavior described on the linked pages.

Count several lanes

z-fastq count lane1.fastq.gz lane2.fastq.gz lane3.fastq.gz

One count per input, in order.

Stop when the pairs are broken

z-fastq check --paired R1.fastq.gz R2.fastq.gz || { echo "pairs failed validation" >&2; exit 1; }
z-fastq stats --json R1.fastq.gz > R1.stats.json

Make an interleaved gzip file

z-fastq interleave R1.fastq.gz R2.fastq.gz | gzip > interleaved.fastq.gz

Take a paired subset as two files

z-fastq sample --paired --fraction 0.05 --seed 2025 R1.fastq.gz R2.fastq.gz \
  | z-fastq deinterleave --out1 sub_R1.fastq --out2 sub_R2.fastq -

sample --paired writes one interleaved stream; deinterleave splits it again.

Trim, filter, and report for MultiQC

z-fastq process --gzip \
  --adapter1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \
  --low-quality 15 --max-low-quality-percent 40 --max-n 5 --min-length 15 \
  --pair-duplication --qc-tables qc --qc-summary sample.json \
  --out1 trimmed_R1.fastq.gz --out2 trimmed_R2.fastq.gz R1.fastq.gz R2.fastq.gz
multiqc qc sample.json

These are fastp's default filters; see Processing and Quality control.

Replace a file only on success

Write to a temporary path and move it after a zero exit status; Automation shows the pattern and why it matters.

Related pages

• Automation: exit statuses and partial output, which every recipe relies on.
• Command cheat sheet: every option the recipes use.