From 2f353aea859b2ea61e1d3476be8586430a65633c Mon Sep 17 00:00:00 2001 From: bshifaw Date: Sat, 12 Jan 2019 10:08:41 -0500 Subject: [PATCH] Wdlupdate (#15) * Update README.md * Update germline_single_sample_workflow.hg38.inputs.json minor format changes * removed scattered intervals as its not being used in the workflow, corrected haplotype_scatter_count to 50. Add comment regarding exomes intervals in Readme * added the new HaplotypeCaller tasks. * added a generic options * deleted old structure * Update README.md minor edit * sub_strip_path replaced by basename() because hardcoding the gs:// component makes the WDL assume too much about the platform it will run on * removed ceil() to pass Float type as disk_size for GatherBamFiles * Fix for splitRG task. Disk sizing now takes place within tasks. * removed empty haplotyp map file * removed wording for use on exomes * Update fc wdl import links --- fc_germline_single_sample_workflow.wdl | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) 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 {