Regression Testing With Batch Mode

Batch mode is designed for pipeline regression tests where each workflow run produces several output files.

Create a manifest:

label   file_a  file_b  type
de_table    old/de.tsv  new/de.tsv  deg
counts  old/counts.tsv  new/counts.tsv  counts
peaks   old/peaks.bed   new/peaks.bed   bed

Run the batch check:

pipeconcord batch manifest.tsv --format tsv --output concordance.tsv

Fail CI when any successful comparison falls below a threshold:

pipeconcord batch manifest.tsv --min-concordance 0.95

Use --format html --output concordance.html for review artifacts attached to CI runs.