diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs index 8e28a8ef541..f23615ee7f0 100644 --- a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs +++ b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs @@ -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" } diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl index 43a298f18ab..4d469cbe552 100644 --- a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl +++ b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl @@ -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" @@ -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 } } diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test index b75ef58dabc..8b80bea061e 100644 --- a/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test +++ b/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test @@ -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 } diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test index dab9c516164..fd8b508a221 100644 --- a/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test +++ b/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test @@ -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 } diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test index 441db8748f2..04391e4b2ab 100644 --- a/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test +++ b/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test @@ -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 } diff --git a/src/ci/resources/papi_v2_reference_image_manifest.conf b/src/ci/resources/papi_v2_reference_image_manifest.conf index 8c15fc44636..d31c961e15e 100644 --- a/src/ci/resources/papi_v2_reference_image_manifest.conf +++ b/src/ci/resources/papi_v2_reference_image_manifest.conf @@ -1,4819 +1,346 @@ reference-disk-localization-manifests = [ { - "imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/broad-references-disk-image", - "diskSizeGb" : 500, + "imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/hg38-public-2020-10-26", + "diskSizeGb" : 20, "files" : [ { - "path" : "gcp-public-data--broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta.nhr", - "crc32c" : 407769621 - }, { - "path" : "gcp-public-data--broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta.sa", - "crc32c" : 1902048083 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG00129.disc.txt.gz", - "crc32c" : 3404974518 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG04118.split.txt.gz.tbi", - "crc32c" : 4024172857 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19449.split.txt.gz.tbi", - "crc32c" : 1977253058 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG02272.disc.txt.gz", - "crc32c" : 1166548962 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA21133.disc.txt.gz", - "crc32c" : 1427281614 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG03864.disc.txt.gz.tbi", - "crc32c" : 1529087048 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA20764.disc.txt.gz.tbi", - "crc32c" : 1417763527 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA21102.disc.txt.gz.tbi", - "crc32c" : 1680978475 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG00096.split.txt.gz", - "crc32c" : 1667331591 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA18638.split.txt.gz.tbi", - "crc32c" : 2563684534 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG01112.disc.txt.gz", - "crc32c" : 3289968657 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.pac", - "crc32c" : 299013300 - }, { - "path" : "gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi", - "crc32c" : 1373876197 - }, { - "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.delly_exclusionRegions.shard2.tsv", - "crc32c" : 422023470 - }, { - "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.delly_exclusionRegions.shard6.tsv", - "crc32c" : 2641621150 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_044.wham.HG02002.vcf.gz", - "crc32c" : 61945186 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_113.wham.NA18553.vcf.gz", - "crc32c" : 2270157672 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_088.wham.HG03709.vcf.gz", - "crc32c" : 1143326201 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_116.wham.NA18923.vcf.gz", - "crc32c" : 408469998 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_149.wham.NA20802.vcf.gz", - "crc32c" : 2170731227 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_014.wham.HG00599.vcf.gz", - "crc32c" : 2268306580 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_050.wham.HG02186.vcf.gz", - "crc32c" : 2164894354 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_135.wham.NA19684.vcf.gz", - "crc32c" : 2251666164 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_007.wham.HG00288.vcf.gz", - "crc32c" : 3615266090 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_120.wham.NA18995.vcf.gz", - "crc32c" : 851480900 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_024.wham.HG01344.vcf.gz", - "crc32c" : 1569598141 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_080.manta.HG03449.vcf.gz", - "crc32c" : 3827948923 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_081.manta.HG03472.vcf.gz", - "crc32c" : 1026539483 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_006.manta.HG00277.vcf.gz", - "crc32c" : 3528734581 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_116.manta.NA18923.vcf.gz", - "crc32c" : 1495065630 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_062.manta.HG02586.vcf.gz", - "crc32c" : 1681406320 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_135.manta.NA19684.vcf.gz", - 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"crc32c" : 42990821 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG02002.disc.txt.gz.tbi", - "crc32c" : 3745118809 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA18945.disc.txt.gz", - "crc32c" : 3310721851 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19184.split.txt.gz", - "crc32c" : 3448306521 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19449.disc.txt.gz", - "crc32c" : 4252958454 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG01085.disc.txt.gz", - "crc32c" : 2389602066 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA11894.split.txt.gz.tbi", - "crc32c" : 3846004317 - }, { - "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG02235.disc.txt.gz.tbi", - "crc32c" : 365742494 - 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