Merge branch 'fix-hg19-metadata' into 'dev'

Fix hg19 metadata and tag 0.3.2 Closes CW-5248 See merge request epi2melabs/ont-spectre!17
nanoporetech · Nov 8, 2024 · 069821a · 069821a
2 parents 566b761 + 59b425f
commit 069821a
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,13 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.3.2]
+### Fixed
+- Remove extra character in hg19 metadata file 
+
+### Added
+- System tests of hg002 real variation with hg19 reference
+
 ## [v0.3.1]
 ### Changed
 - This is a housekeeping release to update the ont-spectre conda package requirements.

diff --git a/spectre/__init__.py b/spectre/__init__.py
@@ -1 +1 @@
-__version__ = "0.3.1"
+__version__ = "0.3.2"
diff --git a/spectre/data/hg19_metadata.mdr b/spectre/data/hg19_metadata.mdr
@@ -569,4 +569,4 @@ NSPOS	chrY	23901000	23952000
 NSPOS	chrY	28819000	58820000
 NSPOS	chrY	58917000	58968000
 NSPOS	chrGL000210.1	9000	11000
-NSPOS	chrGL000197.1	23000	24000s
+NSPOS	chrGL000197.1	23000	24000
diff --git a/tests/data/system_tests/hg002_chr18_realvar_hg19/expected.bed b/tests/data/system_tests/hg002_chr18_realvar_hg19/expected.bed
@@ -0,0 +1 @@
+18	75152000	75392000	DEL
diff --git a/tests/data/system_tests/hg002_chr18_realvar_hg19/expected.vcf.gz b/tests/data/system_tests/hg002_chr18_realvar_hg19/expected.vcf.gz
diff --git a/tests/data/system_tests/hg002_chr18_realvar_hg19/expected.vcf.gz.tbi b/tests/data/system_tests/hg002_chr18_realvar_hg19/expected.vcf.gz.tbi
diff --git a/...s/hg002_chr18_realvar/input/blacklist.bed → ...02_chr18_realvar_hg19/input/blacklist.bed b/...s/hg002_chr18_realvar/input/blacklist.bed → ...02_chr18_realvar_hg19/input/blacklist.bed
diff --git a/...ts/hg002_chr18_realvar/input/metadata.mdr → ...002_chr18_realvar_hg19/input/metadata.mdr b/...ts/hg002_chr18_realvar/input/metadata.mdr → ...002_chr18_realvar_hg19/input/metadata.mdr
diff --git a/tests/data/system_tests/hg002_chr18_realvar_hg19/input/mosdepth/SAMPLE.mosdepth.summary.txt b/tests/data/system_tests/hg002_chr18_realvar_hg19/input/mosdepth/SAMPLE.mosdepth.summary.txt
@@ -0,0 +1,5 @@
+chrom	length	bases	mean	min	max
+18	78077248	3089503474	39.570	0	4899
+18_region	78077248	3089503474	39.570	0	4899
+total	78077248	3089503474	39.570	0	4899
+total_region	78077248	3089503474	39.570	0	4899
diff --git a/tests/data/system_tests/hg002_chr18_realvar_hg19/input/mosdepth/SAMPLE.regions.bed.gz b/tests/data/system_tests/hg002_chr18_realvar_hg19/input/mosdepth/SAMPLE.regions.bed.gz
diff --git a/tests/data/system_tests/hg002_chr18_realvar_hg19/input/ref.fna.gz b/tests/data/system_tests/hg002_chr18_realvar_hg19/input/ref.fna.gz
diff --git a/tests/data/system_tests/hg002_chr18_realvar_hg19/input/wf_snp.vcf.gz b/tests/data/system_tests/hg002_chr18_realvar_hg19/input/wf_snp.vcf.gz
diff --git a/tests/data/system_tests/hg002_chr19_simulations/input/blacklist.bed b/tests/data/system_tests/hg002_chr19_simulations/input/blacklist.bed
diff --git a/tests/data/system_tests/hg002_chr19_simulations/input/metadata.mdr b/tests/data/system_tests/hg002_chr19_simulations/input/metadata.mdr
diff --git a/tests/system_tests.sh b/tests/system_tests.sh
@@ -3,6 +3,7 @@ set -euo pipefail
 
 declare -a data=( 
     "hg002_chr18_realvar"
+    "hg002_chr18_realvar_hg19"
     "hg002_chr19_simulations"
 )
 
@@ -15,7 +16,17 @@ do
     pfx="tests/data/system_tests/$sample/"
     echo "Data path prefix: $pfx"
 
-    # spectre cleanup and run
+    if [[ "$sample" == *"hg19"* ]]; then
+        metadata="hg19_metadata"
+        blacklist="hg19_blacklist_v1.0"
+    else
+        metadata="hg38_metadata"
+        blacklist="hg38_blacklist_v1.0"
+    fi
+
+    echo "Using metadata: $metadata"
+    echo "Using blacklist: $blacklist"
+
     rm -rf $pfx/output_spectre
     spectre CNVCaller \
             --bin-size 1000 \
@@ -24,8 +35,8 @@ do
             --sample-id sample \
             --output-dir $pfx/output_spectre \
             --reference $pfx/input/ref.fna.gz \
-            --metadata $pfx/input/metadata.mdr \
-            --blacklist $pfx/input/blacklist.bed
+            --metadata $metadata \
+            --blacklist $blacklist
 
     # gziping and indexing for truvari input
     vcf_output="$pfx/output_spectre/sample.vcf"
@@ -52,6 +63,4 @@ do
         exit 1
     fi
 
-done
-
-
+done