From d547fc8f78832698752fbf8fd75b57f482932a21 Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Fri, 9 Oct 2026 18:29:22 +0100
Subject: Add paper workflow.

This workflow is used to compute the results in the paper.
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 paper-2026/README.md | 26 ++++++++++++++++++++++++++
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(limited to 'paper-2026/README.md')

diff --git a/paper-2026/README.md b/paper-2026/README.md
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+To replicate the results in the paper, please follow the instructions below. Guix is required.
+
+# Download data
+Download https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/pggb/chroms/chr8.hprc-v1.0-pggb.gfa.gz and gunzip it.
+```
+wget https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/pggb/chroms/chr8.hprc-v1.0-pggb.gfa.gz
+gunzip chr8.hprc-v1.0-pggb.gfa.gz
+```
+
+# Install software
+Drop into an environment with all the software installed.
+```
+guix time-machine -C channels.scm -- shell -m manifest.scm
+```
+
+# Compile the ccwl workflow
+Compile the ccwl workflow into CWL.
+```
+ccwl compile benchmark.scm -o benchmark.cwl
+```
+
+# Run it
+Run the CWL workflow using ravanan. If you need to add additional arguments so it runs on your HPC cluster, please do so.
+```
+ravanan --guix-channels=channels.scm --store=store benchmark.cwl benchmark-inputs.yaml
+```
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