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output_definition.json
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{
"files": {
"workflow-alignment-stats-report": {
"filepath": "{{ alias }}.wf-somatic-variation-readQC-report.html",
"title": "Workflow alignment statistics report",
"description": "Report of the alignment statistics for each tumor/normal paired sample.",
"mime-type": "text/html",
"optional": false,
"type": "per-sample"
},
"workflow-snv-report": {
"filepath": "{{ alias }}.wf-somatic-snv-report.html",
"title": "Workflow SNV report",
"description": "Report of the SNV for each tumor/normal paired sample.",
"mime-type": "text/html",
"optional": true,
"type": "per-sample"
},
"workflow-sv-report": {
"filepath": "{{ alias }}.wf-somatic-sv-report.html",
"title": "Workflow SV report",
"description": "Report of the SV for each tumor/normal paired sample.",
"mime-type": "text/html",
"optional": true,
"type": "per-sample"
},
"workflow-mod-report": {
"filepath": "{{ alias }}.wf-somatic-mod-report.html",
"title": "Workflow MOD report",
"description": "Report of the modified bases for each tumor/normal paired sample.",
"mime-type": "text/html",
"optional": true,
"type": "per-sample"
},
"snv-vcf": {
"filepath": "{{ alias }}.wf-somatic-snv.vcf.gz",
"title": "Somatic short variant VCF",
"description": "VCF file with the somatic SNVs for the sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"snv-vcf-index": {
"filepath": "{{ alias }}.wf-somatic-snv.vcf.gz.tbi",
"title": "Somatic short variant VCF index",
"description": "The index of the resulting VCF file with the somatic SNVs for the sample.",
"mime-type": "application/octet-stream",
"optional": true,
"type": "per-sample"
},
"sv-vcf": {
"filepath": "{{ alias }}.wf-somatic-sv.vcf.gz",
"title": "Somatic structural variant VCF",
"description": "VCF file with the somatic SVs for the sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"sv-vcf-index": {
"filepath": "{{ alias }}.wf-somatic-sv.vcf.gz.tbi",
"title": "Somatic structural variant VCF index",
"description": "The index of the resulting VCF file with the somatic SVs for the sample.",
"mime-type": "application/octet-stream",
"optional": true,
"type": "per-sample"
},
"mod-bedmethyl-normal": {
"filepath": "{{ alias }}.wf-somatic-mod.normal.bedmethyl.gz",
"title": "Modified bases BEDMethyl (normal)",
"description": "BED file with the aggregated modification counts for the normal sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"mod-summary-normal": {
"filepath": "{{ alias }}.normal.mod_summary.tsv",
"title": "Modified bases summary (normal)",
"description": "Summary modification stats for the normal sample.",
"mime-type": "text/txt",
"optional": true,
"type": "per-sample"
},
"per-mod-type-bedmethyl-normal": {
"filepath": "{{ alias }}/mod/{{ mod type }}/bedMethyl/{{ mod type }}.{{ alias }}.wf-somatic-mod.normal.bedmethyl.gz",
"title": "Single-change BEDMethyl (normal)",
"description": "BED file with the aggregated modification counts for a single modification type (e.g. 5mc) for the normal sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"per-mod-type-dss-normal": {
"filepath": "{{ alias }}/mod/{{ mod type }}/DSS/{{ mod type }}.{{ alias }}_normal.dss.tsv",
"title": "Single-change DSS input file (normal)",
"description": "Input text file for DSS for a single modification type (e.g. 5mc) for the normal sample.",
"mime-type": "text/txt",
"optional": true,
"type": "per-sample"
},
"mod-bedmethyl-tumor": {
"filepath": "{{ alias }}.wf-somatic-mod.tumor.bedmethyl.gz",
"title": "Modified bases BEDMethyl (tumor)",
"description": "BED file with the aggregated modification counts for the tumor sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"mod-summary-tumor": {
"filepath": "{{ alias }}.normal.mod_summary.tsv",
"title": "Modified bases summary (tumor)",
"description": "Summary modification stats for the tumor sample.",
"mime-type": "text/txt",
"optional": true,
"type": "per-sample"
},
"per-mod-type-bedmethyl-tumor": {
"filepath": "{{ alias }}/mod/{{ mod type }}/bedMethyl/{{ mod type }}.{{ alias }}.wf-somatic-mod.tumor.bedmethyl.gz",
"title": "Single-change BEDMethyl (tumor)",
"description": "BED file with the aggregated modification counts for a single modification type (e.g. 5mc) for the tumor sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"per-mod-type-dss-tumor": {
"filepath": "{{ alias }}/mod/{{ mod type }}/DSS/{{ mod type }}.{{ alias }}_tumor.dss.tsv",
"title": "Single-change DSS input file (tumor)",
"description": "Input text file for DSS for a single modification type (e.g. 5mc) for the tumor sample.",
"mime-type": "text/txt",
"optional": true,
"type": "per-sample"
},
"per-mod-type-differentially-modified-loci": {
"filepath": "{{ alias }}/mod/{{ mod type }}/DML/{{ alias }}.{{ mod type }}.dml.tsv",
"title": "Differentially modified loci (DML) per change type",
"description": "Differentially modified loci from DSS for a single modification type (e.g. 5mc).",
"mime-type": "text/txt",
"optional": true,
"type": "per-sample"
},
"per-mod-type-differentially-modified-region": {
"filepath": "{{ alias }}/mod/{{ mod type }}/DMR/{{ alias }}.{{ mod type }}.dmr.tsv",
"title": "Differentially modified regions (DMR) per change type",
"description": "Differentially modified regions from DSS for a single modification type (e.g. 5mc).",
"mime-type": "text/txt",
"optional": true,
"type": "per-sample"
},
"alignment-normal": {
"filepath": "{{ alias }}/bam/normal/reads.bam",
"title": "Alignment file (normal)",
"description": "BAM or CRAM file with the aligned reads for the normal sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"alignment-index-normal": {
"filepath": "{{ alias }}/bam/normal/reads.bam.bai",
"title": "Alignment file index (normal)",
"description": "The index of the resulting BAM or CRAM file with the aligned reads for the normal sample.",
"mime-type": "application/octet-stream",
"optional": true,
"type": "per-sample"
},
"alignment-tumor": {
"filepath": "{{ alias }}/bam/tumor/reads.bam",
"title": "Alignment file (tumor)",
"description": "BAM or CRAM file with the aligned reads for the tumor sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"alignment-index-tumor": {
"filepath": "{{ alias }}/bam/tumor/reads.bam.bai",
"title": "Alignment file index (tumor)",
"description": "The index of the resulting BAM or CRAM file with the aligned reads for the tumor sample.",
"mime-type": "application/octet-stream",
"optional": true,
"type": "per-sample"
},
"haplotagged-alignment-normal": {
"filepath": "{{ alias }}_normal.ht.bam",
"title": "Haplotagged alignment file (normal)",
"description": "BAM or CRAM file with the haplotagged reads for the normal sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"haplotagged-alignment-index-normal": {
"filepath": "{{ alias }}_normal.ht.bam.bai",
"title": "Haplotagged alignment file index (normal)",
"description": "The index of the resulting BAM or CRAM file with the haplotagged reads for the normal sample.",
"mime-type": "application/octet-stream",
"optional": true,
"type": "per-sample"
},
"haplotagged-alignment-tumor": {
"filepath": "{{ alias }}_tumor.ht.bam",
"title": "Haplotagged alignment file (tumor)",
"description": "BAM or CRAM file with the haplotagged reads for the tumor sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"haplotagged-alignment-index-tumor": {
"filepath": "{{ alias }}_tumor.ht.bam.bai",
"title": "Haplotagged alignment file index (tumor)",
"description": "The index of the resulting BAM or CRAM file with the haplotagged reads for the tumor sample.",
"mime-type": "application/octet-stream",
"optional": true,
"type": "per-sample"
}
}
}