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include required(classpath("application")) | |
google { | |
application-name = "cromwell" | |
auths = [ | |
{ | |
name = "application-default" | |
scheme = "application_default" |
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#!/bin/bash | |
echo ================================== | |
echo =========== MONITORING =========== | |
echo ================================== | |
echo --- General Information --- | |
echo \#CPU: $(nproc) | |
echo Total Memory: $(free -h | grep Mem | awk '{ print $2 }') | |
echo Total Disk space: $(df -h | grep cromwell_root | awk '{ print $2}') | |
echo | |
echo --- Runtime Information --- |
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workflow HelloWorld { | |
call echo {} | |
} | |
task echo { | |
command { echo hello world! } | |
runtime { | |
docker: "ubuntu:latest" | |
} | |
output { |
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cwlVersion: v1.0 | |
class: Workflow | |
label: "Hello World" | |
doc: "Outputs a message using echo" | |
inputs: [] | |
requirements: | |
- class: DockerRequirement |
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backend { | |
# Override the default backend. | |
default = "LocalExample" | |
# The list of providers. | |
providers { | |
# The local provider is included by default in the reference.conf. This is an example. | |
# Define a new backend provider. |
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## This is the TopMed alignment workflow WDL for the workflow code located here: | |
## https://github.com/statgen/docker-alignment | |
## | |
## NOTE: | |
## The reference genome files to use are located here: | |
## ftp://share.sph.umich.edu/gotcloud/ref/hs38DH-db142-v1.tgz | |
## | |
## You can get the dbSNP reference files that the post align task uses at: | |
## gs://topmed-irc-share/resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz | |
## gs://topmed-irc-share/resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi |
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task print { | |
File inFile | |
command { | |
cat ${inFile} | |
} | |
output { | |
String contents = read_string(stdout()) | |
} | |
runtime { | |
docker: "ubuntu@sha256:71cd81252a3563a03ad8daee81047b62ab5d892ebbfbf71cf53415f29c130950" |
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{ | |
"wf_hello.print.inFile": "gs://rm-dev/a.txt" | |
} |
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## Copyright Broad Institute, 2018 | |
## | |
## This WDL pipeline implements data pre-processing according to the GATK Best Practices | |
## (June 2016). | |
## | |
## Requirements/expectations : | |
## - Pair-end sequencing data in unmapped BAM (uBAM) format | |
## - One or more read groups, one per uBAM file, all belonging to a single sample (SM) | |
## - Input uBAM files must additionally comply with the following requirements: | |
## - - filenames all have the same suffix (we use ".unmapped.bam") |
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workflow test_gpu_wf { | |
call test_gpu {} | |
} | |
task test_gpu { | |
command { nvidia-smi } | |
runtime { | |
gpuType: "nvidia-tesla-k80" | |
gpuCount: 1 |
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