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checker_workflow.wdl
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checker_workflow.wdl
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# GEM version 1.4.1
import "gem_workflow.wdl" as gem_wf
workflow checker {
Array[File] bgenfiles
Float maf
File phenofile
String sample_id_header
String outcome
String exposure_names
String int_covar_names
String covar_names
String missing
Boolean robust
Int memory
Int disk
File expected_sumstats
call gem_wf.run_GEM {
input:
bgenfiles = bgenfiles,
maf = maf,
phenofile = phenofile,
sample_id_header = sample_id_header,
outcome = outcome,
exposure_names = exposure_names,
int_covar_names = int_covar_names,
covar_names = covar_names,
missing = missing,
robust = robust,
memory = memory,
disk = disk
}
call md5sum {
input:
sumstats = run_GEM.gem_results,
expected_sumstats = expected_sumstats
}
meta {
author: "Kenny Westerman"
email: "[email protected]"
}
}
task md5sum {
File sumstats
File expected_sumstats
command <<<
md5sum ${sumstats} > sum.txt
md5sum ${expected_sumstats} > expected_sum.txt
# temporarily outputting to stderr for clarity's sake
>&2 echo "Output checksum:"
>&2 cat sum.txt
>&2 echo "-=-=-=-=-=-=-=-=-=-"
>&2 echo "Truth checksum:"
>&2 cat expected_sum.txt
>&2 echo "-=-=-=-=-=-=-=-=-=-"
>&2 echo "Head of the output file:"
>&2 head ${sumstats}
>&2 echo "-=-=-=-=-=-=-=-=-=-"
>&2 echo "Head of the truth file:"
>&2 head ${expected_sumstats}
echo "$(cut -f1 -d' ' expected_sum.txt) ${sumstats}" | md5sum --check
>>>
runtime {
docker: "quay.io/large-scale-gxe-methods/ubuntu:focal-20210325"
}
}