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broadinstitute · Jun 5, 2018 · 30b487d · 30b487d
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commit 30b487d
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diff --git a/scripts/mutect2_wdl/mutect2.wdl b/scripts/mutect2_wdl/mutect2.wdl
@@ -41,6 +41,7 @@
 ## onco_ds_tar_gz, default_config_file: Oncotator datasources and config file
 ## sequencing_center, sequence_source: metadata for Oncotator
 ## filter_oncotator_maf: Whether the MAF generated by oncotator should have the filtered variants removed. Default: true
+## realignment_index_bundle: resource for FilterAlignmentArtifacts, which runs if and only if it is specified.  Generated by BwaMemIndexImageCreator.
 ##
 ## Outputs :
 ## - One VCF file and its index with primary filtering applied; secondary filtering and functional annotation if requested; a bamout.bam

diff --git a/scripts/mutect2_wdl/mutect2_nio.wdl b/scripts/mutect2_wdl/mutect2_nio.wdl
@@ -45,6 +45,7 @@
 ## onco_ds_tar_gz, default_config_file: Oncotator datasources and config file
 ## sequencing_center, sequence_source: metadata for Oncotator
 ## filter_oncotator_maf: Whether the MAF generated by oncotator should have the filtered variants removed. Default: true
+## realignment_index_bundle: resource for FilterAlignmentArtifacts, which runs if and only if it is specified.  Generated by BwaMemIndexImageCreator.
 ##
 ## Outputs :
 ## - One VCF file and its index with primary filtering applied; secondary filtering and functional annotation if requested; a bamout.bam