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authorArun Isaac2026-10-09 18:29:22 +0100
committerArun Isaac2026-10-09 18:29:22 +0100
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Add paper workflow. HEAD paper-2026-workflow main
This workflow is used to compute the results in the paper.
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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
+```