rm LDPRE

Daylily-Informatics · Nov 17, 2024 · b4d5883 · b4d5883
1 parent 80fb050
commit b4d5883
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/config/supporting_files/b37_supporting_files.yaml b/config/supporting_files/b37_supporting_files.yaml
@@ -5,7 +5,7 @@ supporting_files:   ## All of this structure was for an exploratory, now depreca
     huref:
       ref:
         class: file_no_suffix_star          # This is for use with local copy and webdav copy. These dirs contain other share resources that don't need to be dragged around unecessarily
-        name: /fsx/data/genomic_data/organism_references/H_sapiens/b37/human_1kg_v37/human_1kg_v37.fasta.gz
+        name: /fsx/data/genomic_data/organism_references/H_sapiens/b37/human_1kg_v37/human_1kg_v37.fasta
       genome_file:
         class: file_no_suffix_star
         name: /fsx/data/genomic_data/organism_references/H_sapiens/b37/human_1kg_v37/human_1kg_v37.genome

diff --git a/config/supporting_files/hg38_supporting_files.yaml b/config/supporting_files/hg38_supporting_files.yaml
@@ -8,7 +8,7 @@ supporting_files:   ## All of this structure was for an exploratory, now depreca
         name: /fsx/data/genomic_data/organism_references/H_sapiens/hg38/fasta_fai_minalt/GRCh38_no_alt_analysis_set.fasta
       genome_file:
         class: file_no_suffix_star
-        name: /fsx/data/genomic_data/organism_references/H_sapiens/fasta_fai_minalt/GRCh38_no_alt_analysis_set.fasta
+        name: /fsx/data/genomic_data/organism_references/H_sapiens/hg38/fasta_fai_minalt/GRCh38_no_alt_analysis_set.fasta
       fasta_orig:
         class: file_no_suffix_star
         name: /fsx/data/genomic_data/organism_references/H_sapiens/hg38/fasta_fai_minalt/GRCh38_no_alt_analysis_set.fasta

diff --git a/workflow/rules/dysgu_sv.smk b/workflow/rules/dysgu_sv.smk
@@ -14,7 +14,7 @@ rule dysgu:
     output:
         vcf = MDIR + "{sample}/align/{alnr}/sv/dysgu/{sample}.{alnr}.dysgu.sv.vcf",
     params:
-        huref=config["supporting_files"]["files"]["huref"]["ref"]["name"],
+        huref=config["supporting_files"]["files"]["huref"]["fasta"]["name"],
         min_sv_size="30" if "dysgu" not in config else config["dysgu"]["min_sv_size"],
         cluster_sample=ret_sample_alnr,
         ld_p=config['malloc_alt']['ld_preload'] if 'ld_preload' not in config['dysgu'] else config['dysgu']['ld_preload'],