feat: bump ngs-chew to 0.7 (#334)

bihealth · Jan 10, 2023 · 7f1fa1a · 7f1fa1a
1 parent 1c09320
commit 7f1fa1a
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 9 deletions.
diff --git a/snappy_wrappers/wrappers/ngs_chew/fingerprint/environment.yaml b/snappy_wrappers/wrappers/ngs_chew/fingerprint/environment.yaml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - ngs-chew >=0.6.0,<0.7.0
+  - ngs-chew >=0.7.0,<0.8.0
diff --git a/snappy_wrappers/wrappers/ngs_chew/fingerprint/wrapper.py b/snappy_wrappers/wrappers/ngs_chew/fingerprint/wrapper.py
@@ -6,12 +6,6 @@
 __author__ = "Manuel Holtgrewe"
 __email__ = "manuel.holtgrewe@bih-charite.de"
 
-path_ref = snakemake.config["static_data_config"]["reference"]["path"]
-if "hg19" in path_ref or "37" in path_ref:
-    genome_release = "GRCh37"
-else:
-    genome_release = "GRCh38"
-
 shell(
     r"""
 set -x
@@ -46,8 +40,7 @@
     --reference {snakemake.config[static_data_config][reference][path]} \
     --output-aafs \
     --output-fingerprint {snakemake.output.npz} \
-    --input-bam {snakemake.input.bam} \
-    --genome-release {genome_release}
+    --input-bam {snakemake.input.bam}
 
 pushd $(dirname {snakemake.output.npz})
 md5sum $(basename {snakemake.output.npz}) >$(basename {snakemake.output.npz_md5})