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example_input.json
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example_input.json
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{
"refFile": {
"path": "/media/sshorser/data/oxog_ref_data/full_refdata/public/Homo_sapiens_assembly19.fasta",
"class": "File"
},
"tumourBams": [
{
"path": "/media/sshorser/Data/oxog_test_data_2/DO52739/files_for_workflow/7676725d9976424c98f7a92075e65554.bam",
"class": "File"
},
{
"path": "/media/sshorser/Data/oxog_test_data_2/DO52739/files_for_workflow/dd8bd66c1eb529745a55ae9fea2ddd4b.bam",
"class": "File"
}
],
"normalBam": {
"path": "/media/sshorser/Data/oxog_test_data_2/DO52739/files_for_workflow/6a40a6df68474d9357bacc988ea3e30e.bam",
"class": "File"
},
"tumours":
[
{
"tumourId": "7676725d9976424c98f7a92075e65554",
"bamFileName": "7676725d9976424c98f7a92075e65554.bam",
"associatedVcfs":
[
"f8f0136b-09ec-d079-e040-11ac0c4842e7.broad-mutect-v3.20160222.somatic.snv_mnv.vcf.gz",
"f8f0136b-09ec-d079-e040-11ac0c4842e7.broad-dRanger_snowman-10.20160101.somatic.sv.vcf.gz",
"f8f0136b-09ec-d079-e040-11ac0c4842e7.broad-snowman-10.20160101.somatic.indel.vcf.gz",
"f8f0136b-09ec-d079-e040-11ac0c4842e7.dkfz-snvCalling_1-0-132-1-hpc.1602051320.somatic.snv_mnv.vcf.gz",
"f8f0136b-09ec-d079-e040-11ac0c4842e7.dkfz-indelCalling_1-0-132-1-hpc.1602051320.somatic.indel.vcf.gz",
"f8f0136b-09ec-d079-e040-11ac0c4842e7.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf.gz",
"f8f0136b-09ec-d079-e040-11ac0c4842e7.MUSE_1-0rc-b391201-vcf.20160101.somatic.snv_mnv.vcf.gz",
"f8f0136b-09ec-d079-e040-11ac0c4842e7.svcp_1-0-5.20150306.somatic.snv_mnv.vcf.gz",
"f8f0136b-09ec-d079-e040-11ac0c4842e7.svcp_1-0-5.20150306.somatic.indel.vcf.gz",
"f8f0136b-09ec-d079-e040-11ac0c4842e7.svfix2_4-0-12.20160213.somatic.sv.vcf.gz"
],
"oxoQScore":51.89
}
,
{
"tumourId": "dd8bd66c1eb529745a55ae9fea2ddd4b",
"bamFileName": "dd8bd66c1eb529745a55ae9fea2ddd4b.bam",
"associatedVcfs":
[
"f8e61a02-938b-9428-e040-11ac0d481b6c.broad-mutect-v3.20160222.somatic.snv_mnv.vcf.gz",
"f8e61a02-938b-9428-e040-11ac0d481b6c.broad-dRanger_snowman-10.20160101.somatic.sv.vcf.gz",
"f8e61a02-938b-9428-e040-11ac0d481b6c.broad-snowman-10.20160101.somatic.indel.vcf.gz",
"f8e61a02-938b-9428-e040-11ac0d481b6c.dkfz-snvCalling_1-0-132-1-hpc.1602051320.somatic.snv_mnv.vcf.gz",
"f8e61a02-938b-9428-e040-11ac0d481b6c.dkfz-indelCalling_1-0-132-1-hpc.1602051320.somatic.indel.vcf.gz",
"f8e61a02-938b-9428-e040-11ac0d481b6c.embl-delly_1-0-0-preFilter-hpc.150901.somatic.sv.vcf.gz",
"f8e61a02-938b-9428-e040-11ac0d481b6c.MUSE_1-0rc-b391201-vcf.20160101.somatic.snv_mnv.vcf.gz",
"f8e61a02-938b-9428-e040-11ac0d481b6c.svcp_1-0-5.20150306.somatic.indel.vcf.gz",
"f8e61a02-938b-9428-e040-11ac0d481b6c.svcp_1-0-5.20150306.somatic.snv_mnv.vcf.gz",
"f8e61a02-938b-9428-e040-11ac0d481b6c.svfix2_4-0-12.20160213.somatic.sv.vcf.gz"
],
"oxoQScore":45.65
}
],
"out_dir": "/var/spool/cwl/",
"inputFileDirectory": {
"class":"Directory",
"path":"/media/sshorser/Data/oxog_test_data_2/DO52739/files_for_workflow",
"location":"/media/sshorser/Data/oxog_test_data_2/DO52739/files_for_workflow"
},
"oxogVCFs":
[
{
"path": "/media/sshorser/Data/oxog_only_wf/f8e61a02-938b-9428-e040-11ac0d481b6c.svcp_1-0-5.20150306.somatic.snv_mnv.pass-filtered.cleaned.oxoG.vcf.gz",
"class": "File"
},
{
"path": "/media/sshorser/Data/oxog_only_wf/f8e61a02-938b-9428-e040-11ac0d481b6c.MUSE_1-0rc-b391201-vcf.20160101.somatic.snv_mnv.cleaned.oxoG.vcf.gz",
"class": "File"
},
{
"path": "/media/sshorser/Data/oxog_only_wf/f8e61a02-938b-9428-e040-11ac0d481b6c.dkfz-snvCalling_1-0-132-1-hpc.1602051320.somatic.snv_mnv.pass-filtered.cleaned.oxoG.vcf.gz",
"class": "File"
},
{
"path": "/media/sshorser/Data/oxog_only_wf/f8e61a02-938b-9428-e040-11ac0d481b6c.broad-mutect-v3.20160222.somatic.snv_mnv.pass-filtered.cleaned.oxoG.vcf.gz",
"class": "File"
},
{
"path": "/media/sshorser/Data/oxog_only_wf/f8f0136b-09ec-d079-e040-11ac0c4842e7.svcp_1-0-5.20150306.somatic.snv_mnv.pass-filtered.cleaned.oxoG.vcf.gz",
"class": "File"
},
{
"path": "/media/sshorser/Data/oxog_only_wf/f8f0136b-09ec-d079-e040-11ac0c4842e7.MUSE_1-0rc-b391201-vcf.20160101.somatic.snv_mnv.cleaned.oxoG.vcf.gz",
"class": "File"
},
{
"path": "/media/sshorser/Data/oxog_only_wf/f8f0136b-09ec-d079-e040-11ac0c4842e7.dkfz-snvCalling_1-0-132-1-hpc.1602051320.somatic.snv_mnv.pass-filtered.cleaned.oxoG.vcf.gz",
"class": "File"
},
{
"path": "/media/sshorser/Data/oxog_only_wf/f8f0136b-09ec-d079-e040-11ac0c4842e7.broad-mutect-v3.20160222.somatic.snv_mnv.pass-filtered.cleaned.oxoG.vcf.gz",
"class": "File"
}
]
}