From 54ae5c5d438e69b5d9990fbe9d42ee5b0e9c5b04 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 28 Aug 2024 20:46:36 +0200
Subject: [PATCH] fix var names

---
 cg/constants/scout.py                | 2 +-
 cg/models/scout/scout_load_config.py | 9 +++++++--
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/cg/constants/scout.py b/cg/constants/scout.py
index fb2a5443d8..47da27108a 100644
--- a/cg/constants/scout.py
+++ b/cg/constants/scout.py
@@ -103,7 +103,7 @@ class ScoutUploadKey(StrEnum):
 
 RAREDISEASE_SAMPLE_TAGS = dict(
     bam_file={"bam"},
-    alignment_file={"cram"},
+    # alignment_file={"cram"},
     vcf2cytosure={"vcf2cytosure"},
     mt_bam={"bam-mt"},
     chromograph_autozyg={"chromograph", "autozyg"},
diff --git a/cg/models/scout/scout_load_config.py b/cg/models/scout/scout_load_config.py
index 8b7852281a..2eda3028c8 100644
--- a/cg/models/scout/scout_load_config.py
+++ b/cg/models/scout/scout_load_config.py
@@ -69,8 +69,13 @@ class ScoutMipIndividual(ScoutIndividual):
 
 class ScoutRarediseaseIndividual(ScoutIndividual):
     mt_bam: str | None = None
-    chromograph_images: ChromographImages = ChromographImages()
-    reviewer: Reviewer = Reviewer()
+    bam_file: str | None = None
+    chromograph_autozyg: str | None = None
+    chromograph_coverage: str | None = None
+    chromograph_regions: ChromographImages = ChromographImages()
+    chromograph_sites: ChromographImages = ChromographImages()
+    reviewer_alignment: Reviewer = Reviewer()
+    reviewer_alignment_index: Reviewer = Reviewer()
     rhocall_bed: str | None = None
     rhocall_wig: str | None = None
     tiddit_coverage_wig: str | None = None