remove R scripts from filtering (#7781)

* remove R scripts from filtering * add to dockstore for testing
broadinstitute · Apr 14, 2022 · 8a4f8df · 8a4f8df
1 parent 1fecbf9
commit 8a4f8df
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Showing 2 changed files with 1 addition and 5 deletions.
diff --git a/.dockstore.yml b/.dockstore.yml
@@ -89,7 +89,7 @@ workflows:
        branches:
          - master
          - ah_var_store
-         - kc_wdl_gatk_override
+         - rc-remove-r-graphing-from-filter
    - name: GvsCreateAltAllele
      subclass: WDL
      primaryDescriptorPath: /scripts/variantstore/wdl/GvsCreateAltAllele.wdl

diff --git a/scripts/variantstore/wdl/GvsWarpTasks.wdl b/scripts/variantstore/wdl/GvsWarpTasks.wdl
@@ -172,7 +172,6 @@ task IndelsVariantRecalibrator {
         -V ~{sites_only_variant_filtered_vcf} \
         -O ~{recalibration_filename} \
         --output-model indels.model \
-        --rscript-file indels.Rscript \
         --tranches-file ~{tranches_filename} \
         --trust-all-polymorphic \
         -tranche ~{sep=' -tranche ' recalibration_tranche_values} \
@@ -199,7 +198,6 @@ task IndelsVariantRecalibrator {
         File recalibration_index = "~{recalibration_filename}.idx"
         File tranches = "~{tranches_filename}"
         File model = "indels.model"
-        File rscript = "indels.Rscript"
     }
 }
 
@@ -252,7 +250,6 @@ task SNPsVariantRecalibrator {
         -V ~{sites_only_variant_filtered_vcf} \
         -O ~{recalibration_filename} \
         --output-model snps.model \
-        --rscript-file snps.Rscript \
         --tranches-file ~{tranches_filename} \
         --trust-all-polymorphic \
         -tranche ~{sep=' -tranche ' recalibration_tranche_values} \
@@ -281,6 +278,5 @@ task SNPsVariantRecalibrator {
         File recalibration_index = "~{recalibration_filename}.idx"
         File tranches = "~{tranches_filename}"
         File model = "snps.model"
-        File rscript = "snps.Rscript"
     }
 }