From 6f6229cc2960c63ac76a5bd16f2b51c1c4e9fb1d Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 13 Mar 2026 13:56:09 +0000
Subject: [PATCH 1/2] Initial plan


From c70246271d05495d2dcca08d55b9ee5a9d2e1309 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 13 Mar 2026 13:57:20 +0000
Subject: [PATCH 2/2] Add indel_ref_signatures to nextflow_schema.json
 reference_datasets section

Co-authored-by: efigb <154223352+efigb@users.noreply.github.com>
---
 nextflow_schema.json | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index b100be58..3de7241c 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -729,6 +729,15 @@
                     "fa_icon": "far fa-file-code",
                     "default": "COSMIC_v3.4_SBS_GRCh38.txt"
                 },
+                "indel_ref_signatures": {
+                    "type": "string",
+                    "format": "file-path",
+                    "mimetype": "text/plain",
+                    "description": "Path to file containing the reference indel (ID) signatures to use in SigProfilerAssignment.",
+                    "help_text": "You can obtain it from COSMIC website. Note that for ID signatures the GRCh37 genome version is used.",
+                    "fa_icon": "far fa-file-code",
+                    "default": "COSMIC_v3.4_ID_GRCh37.txt"
+                },
                 "wgs_trinuc_counts": {
                     "type": "string",
                     "format": "file-path",