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checker-input-cwl.json
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checker-input-cwl.json
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{
"reads":[
{
"path":"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/hg19.chr22.5x.normal.bam",
"basename": "hg19.chr22.5x.normal.bam",
"class":"File"
},
{
"path":"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/hg19.chr22.5x.normal2.bam",
"basename": "hg19.chr22.5x.normal2.bam",
"class":"File"
}
],
"output_dir":"datastore",
"output_file_basename":"hg19.chr22.5x.normal",
"download_reference_files":"true",
"reference_gz_amb":{
"path":"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz.64.amb",
"basename": "genome.fa.gz.64.amb",
"class":"File"
},
"reference_gz_sa":{
"path":"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz.64.sa",
"basename": "genome.fa.gz.64.sa",
"class":"File"
},
"reference_gz_pac":{
"path":"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz.64.pac",
"basename": "genome.fa.gz.64.pac",
"class":"File"
},
"reference_gz_ann":{
"path":"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz.64.ann",
"basename": "genome.fa.gz.64.ann",
"class":"File"
},
"reference_gz_bwt":{
"path":"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz.64.bwt",
"basename": "genome.fa.gz.64.bwt",
"class":"File"
},
"reference_gz_fai":{
"path":"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz.fai",
"basename": "genome.fa.gz.fai",
"class":"File"
},
"reference_gz":{
"path":"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz",
"basename": "genome.fa.gz",
"class":"File"
},
"reference_result_normal_bam":{
"path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/reference_results/hg19.chr22.5x.normal.bam",
"basename": "reference_results.hg19.chr22.5x.normal.bam",
"class":"File"
},
"reference_result_normal_unmapped_bam":{
"path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/reference_results/hg19.chr22.5x.normal.unmapped.bam",
"basename": "reference_results.hg19.chr22.5x.normal.unmapped.bam",
"class": "File"
},
"reference_result_normal_bai":{
"path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/reference_results/hg19.chr22.5x.normal.bam.bai",
"basename":"reference_results.hg19.chr22.5x.normal.bam.bai",
"class": "File"
},
"reference_result_normal_unmapped_bai": {
"path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/reference_results/hg19.chr22.5x.normal.unmapped.bam.bai",
"basename": "reference_results.hg19.chr22.5x.normal.unmapped.bam.bai",
"class": "File"
},
"reference_result_normal_metrics": {
"path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/reference_results/hg19.chr22.5x.normal.bam.metrics",
"basename": "reference_results.hg19.chr22.5x.normal.bam.metrics",
"class": "File"
},
"reference_result_normal_unmapped_metrics": {
"path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/reference_results/hg19.chr22.5x.normal.unmapped.bam.metrics",
"basename": "reference_results.hg19.chr22.5x.normal.unmapped.bam.metrics",
"class": "File"
}
}