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Add Nirvana 3.18.1 reference image test, minor cleanup [VS-705] #6975

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merged 5 commits into from
Jan 18, 2023
Merged

Add Nirvana 3.18.1 reference image test, minor cleanup [VS-705] #6975

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b60f58f
initial commit, works for Nirvana input
mcovarr Jan 6, 2023
92eed36
cleanup, use broad reference images like those in firecloud-develop
mcovarr Jan 6, 2023
8046b20
CI bump
mcovarr Jan 12, 2023
c65955b
bump
mcovarr Jan 12, 2023
61fbbc1
Poke CI
jgainerdewar Jan 13, 2023
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3 changes: 2 additions & 1 deletion centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs
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@@ -1,3 +1,4 @@
{
"wf_reference_disk_test.check_if_localized_as_symlink.reference_file_input": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.tile_db_header.vcf"
"wf_reference_disk_test.broad_reference_file_input": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
"wf_reference_disk_test.nirvana_reference_file_input": "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd.idx"
}
30 changes: 24 additions & 6 deletions centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
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@@ -1,11 +1,20 @@
version 1.0

task check_if_localized_as_symlink {
File reference_file_input
input {
File broad_reference_file_input
File nirvana_reference_file_input
}
String broad_input_symlink = "broad_input_symlink.txt"
String nirvana_input_symlink = "nirvana_input_symlink.txt"
command {
# print true if file is a symlink, otherwise print false
if test -h ${reference_file_input}; then echo "true"; else echo "false"; fi;
# Print true if input is a symlink, otherwise print false.
if test -h ~{broad_reference_file_input}; then echo true; else echo false; fi > ~{broad_input_symlink}
if test -h ~{nirvana_reference_file_input}; then echo true; else echo false; fi > ~{nirvana_input_symlink}
}
output {
Boolean is_symlink = read_boolean(stdout())
Boolean is_broad_input_symlink = read_boolean("~{broad_input_symlink}")
Boolean is_nirvana_input_symlink = read_boolean("~{nirvana_input_symlink}")
}
runtime {
docker: "ubuntu:latest"
Expand All @@ -14,8 +23,17 @@ task check_if_localized_as_symlink {
}

workflow wf_reference_disk_test {
call check_if_localized_as_symlink
input {
File broad_reference_file_input
File nirvana_reference_file_input
}
call check_if_localized_as_symlink {
input:
broad_reference_file_input = broad_reference_file_input,
nirvana_reference_file_input = nirvana_reference_file_input
}
output {
Boolean is_input_file_a_symlink = check_if_localized_as_symlink.is_symlink
Boolean is_broad_input_file_a_symlink = check_if_localized_as_symlink.is_broad_input_symlink
Boolean is_nirvana_input_file_a_symlink = check_if_localized_as_symlink.is_nirvana_input_symlink
}
}
3 changes: 2 additions & 1 deletion centaur/src/main/resources/standardTestCases/reference_disk_false_options.test
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Expand Up @@ -11,5 +11,6 @@ files {
metadata {
workflowName: wf_reference_disk_test
status: Succeeded
"outputs.wf_reference_disk_test.is_input_file_a_symlink": false
"outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": false
"outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": false
}
3 changes: 2 additions & 1 deletion centaur/src/main/resources/standardTestCases/reference_disk_true_options.test
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Expand Up @@ -11,5 +11,6 @@ files {
metadata {
workflowName: wf_reference_disk_test
status: Succeeded
"outputs.wf_reference_disk_test.is_input_file_a_symlink": true
"outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": true
"outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": true
}
3 changes: 2 additions & 1 deletion centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test
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Expand Up @@ -11,5 +11,6 @@ files {
metadata {
workflowName: wf_reference_disk_test
status: Succeeded
"outputs.wf_reference_disk_test.is_input_file_a_symlink": false
"outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": false
"outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": false
}
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