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varfish-org · Jun 14, 2024 · 2697370 · 2697370
1 parent 0acbb53
commit 2697370
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Showing 5 changed files with 15 additions and 15 deletions.
diff --git a/rules/output/worker/bgdb.smk b/rules/output/worker/bgdb.smk
@@ -12,7 +12,7 @@ rule output_worker_bgdb_g1k:
         varfish-server-worker strucvars txt-to-bin \
             --input-type strucvar-g1k \
             --path-input {input.bed} \
-            --path-output-bin {output.bin}
+            --path-output {output.bin}
 
         varfish-db-downloader tpl \
             --template rules/output/worker/bgdb.spec.yaml \
@@ -43,7 +43,7 @@ rule output_worker_bgdb_exac:
         varfish-server-worker strucvars txt-to-bin \
             --input-type strucvar-exac-cnv \
             --path-input {input.bed} \
-            --path-output-bin {output.bin}
+            --path-output {output.bin}
 
         varfish-db-downloader tpl \
             --template rules/output/worker/bgdb.spec.yaml \
@@ -72,9 +72,9 @@ rule output_worker_bgdb_gnomad_exomes_cnv_grch38:
     shell:
         r"""
         varfish-server-worker strucvars txt-to-bin \
-            --input-type strucvar-gnomad-exomes-cnv4 \
-            --path-in {input.bed} \
-            --path-output-bin {output.bin}
+            --input-type strucvar-gnomad-cnv4 \
+            --path-input {input.bed} \
+            --path-output {output.bin}
 
         varfish-db-downloader tpl \
             --template rules/output/worker/bgdb.spec.yaml \
@@ -105,7 +105,7 @@ rule output_worker_bgdb_gnomad_sv_grch37:
         varfish-server-worker strucvars txt-to-bin \
             --input-type strucvar-gnomad-sv2 \
             --path-input {input.bed} \
-            --path-output-bin {output.bin}
+            --path-output {output.bin}
 
         varfish-db-downloader tpl \
             --template rules/output/worker/bgdb.spec.yaml \
@@ -136,7 +136,7 @@ rule output_worker_bgdb_gnomad_genomes_sv_grch38:
         varfish-server-worker strucvars txt-to-bin \
             --input-type strucvar-gnomad-sv4 \
             --path-input {input.bed} \
-            --path-output-bin {output.bin}
+            --path-output {output.bin}
 
         varfish-db-downloader tpl \
             --template rules/output/worker/bgdb.spec.yaml \
@@ -167,7 +167,7 @@ rule output_worker_bgdb_dbvar:
         varfish-server-worker strucvars txt-to-bin \
             --input-type strucvar-db-var \
             --path-input {input.bed} \
-            --path-output-bin {output.bin}
+            --path-output {output.bin}
 
         varfish-db-downloader tpl \
             --template rules/output/worker/bgdb.spec.yaml \
@@ -198,7 +198,7 @@ rule output_worker_bgdb_dgv:
         varfish-server-worker strucvars txt-to-bin \
             --input-type strucvar-dgv \
             --path-input {input.bed} \
-            --path-output-bin {output.bin}
+            --path-output {output.bin}
 
         varfish-db-downloader tpl \
             --template rules/output/worker/bgdb.spec.yaml \
@@ -229,7 +229,7 @@ rule output_worker_bgdb_dgv_gs:
         varfish-server-worker strucvars txt-to-bin \
             --input-type strucvar-dgv-gs \
             --path-input {input.bed} \
-            --path-output-bin {output.bin}
+            --path-output {output.bin}
 
         varfish-db-downloader tpl \
             --template rules/output/worker/bgdb.spec.yaml \

diff --git a/rules/output/worker/clinvar.smk b/rules/output/worker/clinvar.smk
@@ -26,7 +26,7 @@ rule annos_strucvar_clinvar_convert:
         varfish-server-worker db to-bin \
             --input-type clinvar-sv \
             --path-input {input.tsv} \
-            --path-output-bin {output.bin}
+            --path-output {output.bin}
 
         varfish-db-downloader tpl \
             --template rules/output/worker/clinvar_strucvars.spec.yaml \

diff --git a/rules/output/worker/genes_regions.smk b/rules/output/worker/genes_regions.smk
@@ -20,7 +20,7 @@ rule genes_regions_worker_convert:
             db to-bin \
             --input-type gene-region \
             --path-input {input.bed} \
-            --path-output-bin {output.bin}
+            --path-output {output.bin}
 
         varfish-db-downloader tpl \
             --template rules/output/worker/{wildcards.source}_genes.spec.yaml \

diff --git a/rules/output/worker/hgnc.smk b/rules/output/worker/hgnc.smk
@@ -17,7 +17,7 @@ rule output_hgnc_xlink_binary:
         varfish-server-worker db to-bin \
             --input-type xlink \
             --path-input {input.tsv} \
-            --path-output-bin {output.bin}
+            --path-output {output.bin}
 
         varfish-db-downloader tpl \
             --template rules/output/worker/hgnc_xlink.spec.yaml \

diff --git a/rules/output/worker/masked.smk b/rules/output/worker/masked.smk
@@ -15,7 +15,7 @@ rule output_masked_repeat:
         varfish-server-worker db to-bin \
             --input-type masked-region \
             --path-input {input} \
-            --path-output-bin {output.bin}
+            --path-output {output.bin}
 
         varfish-db-downloader tpl \
             --template rules/output/worker/masked_repeat.spec.yaml \
@@ -44,7 +44,7 @@ rule output_masked_segdup:
         varfish-server-worker db to-bin \
             --input-type masked-region \
             --path-input {input} \
-            --path-output-bin {output.bin}
+            --path-output {output.bin}
 
         varfish-db-downloader tpl \
             --template rules/output/worker/masked_segdup.spec.yaml \