make task robust to reads and index being in different locations. (#6900

) * make task robust to reads and index being in different locations.`
broadinstitute · Jan 12, 2021 · ece7f6a · ece7f6a
1 parent b1aab93
commit ece7f6a
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/scripts/cnn_variant_wdl/cnn_variant_common_tasks.wdl b/scripts/cnn_variant_wdl/cnn_variant_common_tasks.wdl
@@ -41,6 +41,7 @@ command <<<
         gatk --java-options "-Xmx${command_mem}m" \
         CNNScoreVariants \
         ${"-I " + bam_file} \
+        ${"--read-index " + bam_file_index} \
         -R ${reference_fasta} \
         -V ${input_vcf} \
         -O ${output_prefix}_cnn_annotated.vcf.gz \
@@ -104,6 +105,7 @@ task RunHC4 {
         HaplotypeCaller \
         -R ${reference_fasta} \
         -I ${input_bam} \
+        --read-index ${input_bam_index} \
         -O ${output_prefix}_hc4.vcf.gz \
         -L ${interval_list} \
         -bamout ${output_prefix}_bamout.bam \