From 2697370b26f26be7ee2d092e706e0dd905323199 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Tue, 27 Feb 2024 12:49:28 +0100 Subject: [PATCH] wip --- rules/output/worker/bgdb.smk | 20 ++++++++++---------- rules/output/worker/clinvar.smk | 2 +- rules/output/worker/genes_regions.smk | 2 +- rules/output/worker/hgnc.smk | 2 +- rules/output/worker/masked.smk | 4 ++-- 5 files changed, 15 insertions(+), 15 deletions(-) diff --git a/rules/output/worker/bgdb.smk b/rules/output/worker/bgdb.smk index e79ad7c..3caf612 100644 --- 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 index 3230ab5..931d53c 100644 --- 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 index c7cd499..03685c3 100644 --- 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 index 1babd54..6f86df5 100644 --- 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 index 4e46f74..71a6124 100644 --- 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 \