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varfish-org · Jun 14, 2024 · 0ec4a4c · 0ec4a4c
1 parent 2697370
commit 0ec4a4c
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/rules/output/worker/clinvar.smk b/rules/output/worker/clinvar.smk
@@ -23,7 +23,7 @@ rule annos_strucvar_clinvar_convert:
         clinvar_release=RE_VERSION,
     shell:
         r"""
-        varfish-server-worker db to-bin \
+        varfish-server-worker strucvars txt-to-bin \
             --input-type clinvar-sv \
             --path-input {input.tsv} \
             --path-output {output.bin}

diff --git a/rules/output/worker/genes_regions.smk b/rules/output/worker/genes_regions.smk
@@ -17,7 +17,7 @@ rule genes_regions_worker_convert:
     shell:
         r"""
         varfish-server-worker \
-            db to-bin \
+            strucvars txt-to-bin \
             --input-type gene-region \
             --path-input {input.bed} \
             --path-output {output.bin}

diff --git a/rules/output/worker/hgnc.smk b/rules/output/worker/hgnc.smk
@@ -14,7 +14,7 @@ rule output_hgnc_xlink_binary:
             exit 1
         fi
 
-        varfish-server-worker db to-bin \
+        varfish-server-worker strucvars txt-to-bin \
             --input-type xlink \
             --path-input {input.tsv} \
             --path-output {output.bin}

diff --git a/rules/output/worker/masked.smk b/rules/output/worker/masked.smk
@@ -12,7 +12,7 @@ rule output_masked_repeat:
         version=RE_VERSION,
     shell:
         r"""
-        varfish-server-worker db to-bin \
+        varfish-server-worker strucvars txt-to-bin \
             --input-type masked-region \
             --path-input {input} \
             --path-output {output.bin}
@@ -41,7 +41,7 @@ rule output_masked_segdup:
         version=RE_VERSION,
     shell:
         r"""
-        varfish-server-worker db to-bin \
+        varfish-server-worker strucvars txt-to-bin \
             --input-type masked-region \
             --path-input {input} \
             --path-output {output.bin}