From cbb46d83130f4f4a57c689a4652cf575daa7bf1b Mon Sep 17 00:00:00 2001 From: bshifaw Date: Thu, 14 Mar 2019 18:17:53 +0000 Subject: [PATCH] shifted imports to git release 1.0.3 --- fc_germline_single_sample_workflow.wdl | 15 ++++++++------- germline_single_sample_workflow.wdl | 13 +++++++++---- tasks_pipelines/split_large_readgroup.wdl | 6 +++--- tasks_pipelines/unmapped_bam_to_aligned_bam.wdl | 10 +++++----- 4 files changed, 25 insertions(+), 19 deletions(-) diff --git a/fc_germline_single_sample_workflow.wdl b/fc_germline_single_sample_workflow.wdl index dbf02fc..badb467 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 +26,13 @@ ## 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://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines/alignment.wdl" as Alignment +import "https://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines/split_large_readgroup.wdl" as SplitRG +import "https://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines/qc.wdl" as QC +import "https://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines/bam_processing.wdl" as Processing +import "https://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines/germline_variant_discovery.wdl" as Calling +import "https://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines/utilities.wdl" as Utils # WORKFLOW DEFINITION workflow germline_single_sample_workflow { diff --git a/germline_single_sample_workflow.wdl b/germline_single_sample_workflow.wdl index 2ba8400..5d69659 100644 --- a/germline_single_sample_workflow.wdl +++ b/germline_single_sample_workflow.wdl @@ -26,10 +26,15 @@ ## page at https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/ for detailed ## licensing information pertaining to the included programs. -import "./tasks_pipelines/unmapped_bam_to_aligned_bam.wdl" as ToBam -import "./tasks_pipelines/germline_variant_discovery.wdl" as Calling -import "./tasks_pipelines/qc.wdl" as QC -import "./tasks_pipelines/utilities.wdl" as Utils +#import "./tasks_pipelines/unmapped_bam_to_aligned_bam.wdl" as ToBam +#import "./tasks_pipelines/germline_variant_discovery.wdl" as Calling +#import "./tasks_pipelines/qc.wdl" as QC +#import "./tasks_pipelines/utilities.wdl" as Utils + +import "https://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines/unmapped_bam_to_aligned_bam.wdl" as Processing +import "https://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines/germline_variant_discovery.wdl" as Calling +import "https://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines/qc.wdl" as QC +import "https://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines/utilities.wdl" as Utils # WORKFLOW DEFINITION workflow germline_single_sample_workflow { diff --git a/tasks_pipelines/split_large_readgroup.wdl b/tasks_pipelines/split_large_readgroup.wdl index a3044d2..9fa5663 100644 --- a/tasks_pipelines/split_large_readgroup.wdl +++ b/tasks_pipelines/split_large_readgroup.wdl @@ -13,9 +13,9 @@ ## page at https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/ for detailed ## licensing information pertaining to the included programs. -import "./tasks_pipelines/alignment.wdl" as Alignment -import "./tasks_pipelines/bam_processing.wdl" as Processing -import "./tasks_pipelines/utilities.wdl" as Utils +import "https://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines/alignment.wdl" as Alignment +import "https://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines/bam_processing.wdl" as Processing +import "https://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines//utilities.wdl" as Utils workflow split_large_readgroup { File input_bam diff --git a/tasks_pipelines/unmapped_bam_to_aligned_bam.wdl b/tasks_pipelines/unmapped_bam_to_aligned_bam.wdl index 6bb25cd..6819201 100644 --- a/tasks_pipelines/unmapped_bam_to_aligned_bam.wdl +++ b/tasks_pipelines/unmapped_bam_to_aligned_bam.wdl @@ -14,11 +14,11 @@ ## page at https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/ for detailed ## licensing information pertaining to the included programs. -import "./tasks_pipelines/alignment.wdl" as Alignment -import "./tasks_pipelines/split_large_readgroup.wdl" as SplitRG -import "./tasks_pipelines/qc.wdl" as QC -import "./tasks_pipelines/bam_processing.wdl" as Processing -import "./tasks_pipelines/utilities.wdl" as Utils +import "https://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines/alignment.wdl" as Alignment +import "https://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines/split_large_readgroup.wdl" as SplitRG +import "https://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines/qc.wdl" as QC +import "https://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines/bam_processing.wdl" as Processing +import "https://raw.githubusercontent.com/gatk-workflows/five-dollar-genome-analysis-pipeline/1.0.3/tasks_pipelines/utilities.wdl" as Utils # WORKFLOW DEFINITION workflow to_bam_workflow {