diff --git a/fc_germline_single_sample_workflow.wdl b/fc_germline_single_sample_workflow.wdl index dbf02fc..ad461b4 100644 --- a/fc_germline_single_sample_workflow.wdl +++ b/fc_germline_single_sample_workflow.wdl @@ -2,7 +2,7 @@ ## ## This WDL pipeline implements data pre-processing and initial variant calling (GVCF ## generation) according to the GATK Best Practices (June 2016) for germline SNP and -## Indel discovery in human whole-genome. +## Indel discovery in human whole-genome sequencing data. ## ## Requirements/expectations : ## - Human whole-genome pair-end sequencing data in unmapped BAM (uBAM) format @@ -26,12 +26,12 @@ ## page at https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/ for detailed ## licensing information pertaining to the included programs. -import "https://api.firecloud.org/ga4gh/v1/tools/gatk:alignment/versions/2/plain-WDL/descriptor" as Alignment -import "https://api.firecloud.org/ga4gh/v1/tools/gatk:split-large-readgroup/versions/2/plain-WDL/descriptor" as SplitRG -import "https://api.firecloud.org/ga4gh/v1/tools/gatk:quality-control/versions/1/plain-WDL/descriptor" as QC -import "https://api.firecloud.org/ga4gh/v1/tools/gatk:bam-processing/versions/2/plain-WDL/descriptor" as Processing -import "https://api.firecloud.org/ga4gh/v1/tools/gatk:germline-variant-discovery/versions/2/plain-WDL/descriptor" as Calling -import "https://api.firecloud.org/ga4gh/v1/tools/gatk:utilities/versions/1/plain-WDL/descriptor" as Utils +import "https://api.firecloud.org/ga4gh/v1/tools/gatk:alignment/versions/4/plain-WDL/descriptor" as Alignment +import "https://api.firecloud.org/ga4gh/v1/tools/gatk:split-large-readgroup/versions/4/plain-WDL/descriptor" as SplitRG +import "https://api.firecloud.org/ga4gh/v1/tools/gatk:quality-control/versions/2/plain-WDL/descriptor" as QC +import "https://api.firecloud.org/ga4gh/v1/tools/gatk:bam-processing/versions/4/plain-WDL/descriptor" as Processing +import "https://api.firecloud.org/ga4gh/v1/tools/gatk:germline-variant-discovery/versions/3/plain-WDL/descriptor" as Calling +import "https://api.firecloud.org/ga4gh/v1/tools/gatk:utilities/versions/2/plain-WDL/descriptor" as Utils # WORKFLOW DEFINITION workflow germline_single_sample_workflow {