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b5e1b60)
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #
* Variant calling in parallel using GATK Haplotype Caller (https://gatk.broadinstitute.org/hc/en-us)
* Generation of an HTML report comparing variants against ClinVar archive (https://www.ncbi.nlm.nih.gov/clinvar/)
* Variant calling in parallel using GATK Haplotype Caller (https://gatk.broadinstitute.org/hc/en-us)
* Generation of an HTML report comparing variants against ClinVar archive (https://www.ncbi.nlm.nih.gov/clinvar/)
-Workflows are written in CWL v1.1.
+Workflows are written in CWL v1.1. (https://www.commonwl.org/)
Subdirectories are:
* cwl - contains CWL code for the demo
Subdirectories are:
* cwl - contains CWL code for the demo
- arvados-cwl-runner --no-wait --project-uuid YOUR_PROJECT_UUID wgs-processing-wf.cwl ../yml/YOURINPUTS.yml
+ arvados-cwl-runner --no-wait --project-uuid YOUR_PROJECT_UUID ./cwl/wgs-processing-wf.cwl ./yml/YOURINPUTS.yml
About the Demo Data:
WGS Data used in this demo is public data made available by the Personal Genome Project.
About the Demo Data:
WGS Data used in this demo is public data made available by the Personal Genome Project.
outputSource: bwamem-gatk-report/gvcf
format: edam:format_3016 # GVCF
label: GVCFs generated from GATK
outputSource: bwamem-gatk-report/gvcf
format: edam:format_3016 # GVCF
label: GVCFs generated from GATK
report:
type: File[]
outputSource: bwamem-gatk-report/report
report:
type: File[]
outputSource: bwamem-gatk-report/report
--- /dev/null
+fastq1:
+ class: File
+ location: keep:c96565a96cd428fe92bf70e97488bd80+21857/ERR1726424_1.fastq/ERR1726424_1.fastq.gz
+
+fastq2:
+ class: File
+ location: keep:0ea6e3aaa6ead18a2cc4ba67a22939e9+25007/ERR1726424_2.fastq/ERR1726424_2.fastq.gz
bam:
class: File
location: keep:su92l-4zz18-v4m3dx8agdp1y9r/WGC069888D.bam
bam:
class: File
location: keep:su92l-4zz18-v4m3dx8agdp1y9r/WGC069888D.bam
reference:
class: File
location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
reference:
class: File
location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa