diff --git a/cg_hermes/config/balsamic.py b/cg_hermes/config/balsamic.py index 9d6ebb67..bc812241 100644 --- a/cg_hermes/config/balsamic.py +++ b/cg_hermes/config/balsamic.py @@ -10,6 +10,7 @@ "BALSAMIC_X.X.X_graph.pdf": ["balsamic-dag"], "multiqc_report.html": ["html", "multiqc-html"], "multiqc_data.json": ["json", "multiqc-json"], + "tumor.d4": ["d4file", "qc-metrics-d4file"], # Custom QC "metrics_deliverables.yaml": ["yaml", "qc-metrics-yaml"], # Alignment files (PANEL & WGS) @@ -268,6 +269,11 @@ "is_mandatory": True, "used_by": ["audit"], }, + frozenset(RAW_TAGS["tumor.d4"]): { # D4 coverage + "tags": ["d4", "coverage", "tumor"], + "is_mandatory": True, + "used_by": ["scout"], + }, # Custom QC frozenset(RAW_TAGS["metrics_deliverables.yaml"]): { # QC metrics "tags": ["qc-metrics", "deliverable"], diff --git a/tests/fixtures/balsamic/T_panel.hk b/tests/fixtures/balsamic/T_panel.hk index ee020bb0..4b48d139 100644 --- a/tests/fixtures/balsamic/T_panel.hk +++ b/tests/fixtures/balsamic/T_panel.hk @@ -1,219 +1,90 @@ { "files": [ { - "path": "T-panel/analysis/vcf/SNV.somatic.T-panel.vardict.vcf.gz", - "path_index": [ - "T-panel/analysis/vcf/SNV.somatic.T-panel.vardict.vcf.gz.tbi" - ], - "step": "gatk_update_vcf_sequence_dictionary", - "tag": [ - "research-vcf-vardict", - "vcf-vardict" - ], - "id": "T-panel", - "format": "vcf.gz" - }, - { - "path": "T-panel/analysis/vcf/SNV.somatic.T-panel.vardict.vcf.gz.tbi", - "path_index": "", - "step": "gatk_update_vcf_sequence_dictionary", - "tag": [ - "research-vcf-vardict-index", - "vcf-vardict" - ], - "id": "T-panel", - "format": "vcf.gz.tbi" - }, - { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.merged.cadd_indel.research.vcf.gz", - "path_index": [ - "T-panel/analysis/vep/SNV.somatic.T-panel.merged.cadd_indel.research.vcf.gz.tbi" - ], - "step": "vep_annotate_somaticSNV_research", - "tag": [ - "T-panel.merged", - "research-vcf-snv-unfiltered", - "vcf-snv-unfiltered", - "cadd-indel" - ], - "id": "T-panel", - "format": "vcf.gz" - }, - { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.merged.cadd_indel.research.vcf.gz.tbi", - "path_index": "", - "step": "vep_annotate_somaticSNV_research", - "tag": [ - "research-vcf-snv-unfiltered-index", - "T-panel.merged", - "vcf-snv-unfiltered", - "cadd-indel" - ], - "id": "T-panel", - "format": "vcf.gz.tbi" - }, - { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.tnscope_umi.cadd_indel.research.vcf.gz", - "path_index": [ - "T-panel/analysis/vep/SNV.somatic.T-panel.tnscope_umi.cadd_indel.research.vcf.gz.tbi" - ], - "step": "vep_annotate_somaticSNV_research", - "tag": [ - "research-vcf-snv-unfiltered", - "T-panel.tnscope-umi", - "vcf-snv-unfiltered", - "cadd-indel" - ], - "id": "T-panel", - "format": "vcf.gz" - }, - { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.tnscope_umi.cadd_indel.research.vcf.gz.tbi", - "path_index": "", - "step": "vep_annotate_somaticSNV_research", - "tag": [ - "research-vcf-snv-unfiltered-index", - "T-panel.tnscope-umi", - "vcf-snv-unfiltered", - "cadd-indel" - ], - "id": "T-panel", - "format": "vcf.gz.tbi" - }, - { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.merged.research.vcf.gz", - "path_index": [ - "T-panel/analysis/vep/SNV.somatic.T-panel.merged.research.vcf.gz.tbi" - ], - "step": "vep_annotate_somaticSNV_research", - "tag": [ - "merged", - "T-panel", - "vcf-snv-unfiltered", - "research-vcf-snv-unfiltered" - ], - "id": "T-panel", - "format": "vcf.gz" - }, - { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.merged.research.vcf.gz.tbi", - "path_index": "", - "step": "vep_annotate_somaticSNV_research", - "tag": [ - "merged", - "T-panel", - "research-vcf-snv-unfiltered-index", - "vcf-snv-unfiltered" - ], - "id": "T-panel", - "format": "vcf.gz.tbi" - }, - { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.tnscope_umi.research.vcf.gz", - "path_index": [ - "T-panel/analysis/vep/SNV.somatic.T-panel.tnscope_umi.research.vcf.gz.tbi" - ], - "step": "vep_annotate_somaticSNV_research", - "tag": [ - "tnscope-umi", - "T-panel", - "vcf-snv-unfiltered", - "research-vcf-snv-unfiltered" - ], - "id": "T-panel", - "format": "vcf.gz" - }, - { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.tnscope_umi.research.vcf.gz.tbi", - "path_index": "", - "step": "vep_annotate_somaticSNV_research", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vcf/CNV.somatic.T-panel.delly.bcf", + "path_index": [], + "step": "delly_cnv_tumor_only", "tag": [ - "tnscope-umi", - "T-panel", - "research-vcf-snv-unfiltered-index", - "vcf-snv-unfiltered" + "cnv-delly", + "clinical-cnv-delly" ], "id": "T-panel", - "format": "vcf.gz.tbi" + "format": "bcf" }, { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.tnscope_umi_vcfanno_research.toml", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vcf/CNV.somatic.T-panel.dellycnv.cov.gz", "path_index": [], - "step": "vep_annotate_somaticSNV_research", + "step": "delly_cnv_tumor_only", "tag": [ - "tnscope-umi", - "T-panel", - "research-vcfanno-research-toml", - "vcfanno-research-toml" + "rd-delly", + "clinical-rd-delly" ], "id": "T-panel", - "format": "toml" + "format": "gz" }, { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.merged_vcfanno_research.toml", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vcf/CNV.somatic.T-panel.dellycnv.sample_name_map", "path_index": [], - "step": "vep_annotate_somaticSNV_research", + "step": "delly_cnv_tumor_only", "tag": [ - "merged", - "T-panel", - "research-vcfanno-research-toml", - "vcfanno-research-toml" + "namemap", + "clinical-namemap" ], "id": "T-panel", - "format": "toml" + "format": "sample_name_map" }, { - "path": "T-panel/analysis/bam/tumor.tumorsample.cram", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/bam/tumor.tumorsample.cram", "path_index": [ - "T-panel/analysis/bam/tumor.tumorsample.cram.crai" + "/home/proj/stage/cancer/cases/T-panel/analysis/bam/tumor.tumorsample.cram.crai" ], "step": "bam_compress_tumor", "tag": [ - "cram", + "tumor-cram", "tumorsample", - "tumor-cram" + "cram" ], "id": "tumorsample", "format": "cram" }, { - "path": "T-panel/analysis/bam/tumor.tumorsample.cram.crai", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/bam/tumor.tumorsample.cram.crai", "path_index": "", "step": "bam_compress_tumor", "tag": [ - "cram", + "tumor-cram-index", "tumorsample", - "tumor-cram-index" + "cram" ], "id": "tumorsample", "format": "crai" }, { - "path": "T-panel/analysis/vcf/SV.somatic.T-panel.svdb.vcf.gz", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vcf/SV.somatic.T-panel.svdb.vcf.gz", "path_index": [ - "T-panel/analysis/vcf/SV.somatic.T-panel.svdb.vcf.gz.tbi" + "/home/proj/stage/cancer/cases/T-panel/analysis/vcf/SV.somatic.T-panel.svdb.vcf.gz.tbi" ], "step": "svdb_merge_tumor_only", "tag": [ - "research-vcf-svdb", - "vcf-svdb" + "vcf-svdb", + "research-vcf-svdb" ], "id": "T-panel", "format": "vcf.gz" }, { - "path": "T-panel/analysis/vcf/SV.somatic.T-panel.svdb.vcf.gz.tbi", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vcf/SV.somatic.T-panel.svdb.vcf.gz.tbi", "path_index": "", "step": "svdb_merge_tumor_only", "tag": [ - "research-vcf-svdb-index", - "vcf-svdb" + "vcf-svdb", + "research-vcf-svdb-index" ], "id": "T-panel", "format": "vcf.gz.tbi" }, { - "path": "T-panel/analysis/vcf/SV.somatic.T-panel.svdb.sample_name_map", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vcf/SV.somatic.T-panel.svdb.sample_name_map", "path_index": [], "step": "svdb_merge_tumor_only", "tag": [ @@ -224,343 +95,147 @@ "format": "sample_name_map" }, { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.merged.balsamic_stat", - "path_index": [], - "step": "tmb_calculation", - "tag": [ - "research-tmb", - "SNV", - "T-panel", - "merged", - "tmb" - ], - "id": "T-panel", - "format": "balsamic_stat" - }, - { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.tnscope_umi.balsamic_stat", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/cnv/CNV.somatic.T-panel.report.pdf", "path_index": [], - "step": "tmb_calculation", - "tag": [ - "research-tmb", - "SNV", - "T-panel", - "tmb", - "tnscope-umi" - ], - "id": "T-panel", - "format": "balsamic_stat" - }, - { - "path": "T-panel/analysis/vcf/CNV.somatic.T-panel.delly.bcf", - "path_index": [], - "step": "delly_cnv_tumor_only", - "tag": [ - "clinical-cnv-delly", - "cnv-delly" - ], - "id": "T-panel", - "format": "bcf" - }, - { - "path": "T-panel/analysis/vcf/CNV.somatic.T-panel.dellycnv.cov.gz", - "path_index": [], - "step": "delly_cnv_tumor_only", - "tag": [ - "rd-delly", - "clinical-rd-delly" - ], - "id": "T-panel", - "format": "gz" - }, - { - "path": "T-panel/analysis/vcf/CNV.somatic.T-panel.dellycnv.sample_name_map", - "path_index": [], - "step": "delly_cnv_tumor_only", + "step": "merge_cnv_pdf_reports", "tag": [ - "namemap", - "clinical-namemap" + "cnv-report-pdf", + "clinical-cnv-report-pdf" ], "id": "T-panel", - "format": "sample_name_map" + "format": "pdf" }, { - "path": "T-panel/analysis/vep/SV.germline.tumor.manta_germline.vcf.gz", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vcf/SNV.somatic.T-panel.tnscope.vcf.gz", "path_index": [ - "T-panel/analysis/vep/SV.germline.tumor.manta_germline.vcf.gz.tbi" + "/home/proj/stage/cancer/cases/T-panel/analysis/vcf/SNV.somatic.T-panel.tnscope.vcf.gz.tbi" ], - "step": "vep_annotate_germlineVAR_tumor", + "step": "sentieon_tnscope_tga_tumor_only", "tag": [ - "germline-vcf-tumor", - "SV", - "vcf-tumor", - "manta-germline" + "vcf-tnscope", + "research-vcf-tnscope" ], "id": "T-panel", "format": "vcf.gz" }, { - "path": "T-panel/analysis/vep/SV.germline.tumor.manta_germline.vcf.gz.tbi", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vcf/SNV.somatic.T-panel.tnscope.vcf.gz.tbi", "path_index": "", - "step": "vep_annotate_germlineVAR_tumor", + "step": "sentieon_tnscope_tga_tumor_only", "tag": [ - "germline-vcf-tumor-index", - "SV", - "vcf-tumor", - "manta-germline" + "research-vcf-tnscope-index", + "vcf-tnscope" ], "id": "T-panel", "format": "vcf.gz.tbi" }, { - "path": "T-panel/analysis/vep/SNV.germline.tumor.dnascope.vcf.gz", - "path_index": [ - "T-panel/analysis/vep/SNV.germline.tumor.dnascope.vcf.gz.tbi" - ], - "step": "vep_annotate_germlineVAR_tumor", - "tag": [ - "SNV", - "germline-vcf-tumor", - "dnascope", - "vcf-tumor" - ], - "id": "T-panel", - "format": "vcf.gz" - }, - { - "path": "T-panel/analysis/vep/SNV.germline.tumor.dnascope.vcf.gz.tbi", - "path_index": "", - "step": "vep_annotate_germlineVAR_tumor", - "tag": [ - "SNV", - "dnascope", - "vcf-tumor", - "germline-vcf-tumor-index" - ], - "id": "T-panel", - "format": "vcf.gz.tbi" - }, - { - "path": "T-panel/analysis/cnv/tumor.merged.cns", - "path_index": [], - "step": "cnvkit_call_CNV_research", - "tag": [ - "cnv-cns", - "cns" - ], - "id": "T-panel", - "format": "cns" - }, - { - "path": "T-panel/analysis/cnv/T-panel.gene_breaks", - "path_index": [], - "step": "cnvkit_call_CNV_research", - "tag": [ - "cnv-gene-breaks", - "gene-breaks" - ], - "id": "T-panel", - "format": "gene_breaks" - }, - { - "path": "T-panel/analysis/cnv/T-panel.gene_metrics", - "path_index": [], - "step": "cnvkit_call_CNV_research", - "tag": [ - "cnv-gene-metrics", - "gene-metrics" - ], - "id": "T-panel", - "format": "gene_metrics" - }, - { - "path": "T-panel/analysis/cnv/tumor.merged-diagram.pdf", - "path_index": [], - "step": "cnvkit_call_CNV_research", - "tag": [ - "cnv-diagram", - "diagram" - ], - "id": "T-panel", - "format": "pdf" - }, - { - "path": "T-panel/analysis/cnv/tumor.merged-scatter.pdf", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vcf/SNV.somatic.T-panel.tnscope.sample_name_map", "path_index": [], - "step": "cnvkit_call_CNV_research", - "tag": [ - "scatter", - "cnv-scatter" - ], - "id": "T-panel", - "format": "pdf" - }, - { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.merged.clinical.scored.vcf.gz", - "path_index": [ - "T-panel/analysis/vep/SNV.somatic.T-panel.merged.clinical.scored.vcf.gz.tbi" - ], - "step": "genmod_score_snvs", - "tag": [ - "SNV", - "T-panel", - "vcf-clinical", - "merged", - "scored-vcf-clinical" - ], - "id": "T-panel", - "format": "vcf.gz" - }, - { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.merged.clinical.scored.vcf.gz.tbi", - "path_index": "", - "step": "genmod_score_snvs", + "step": "sentieon_tnscope_tga_tumor_only", "tag": [ - "SNV", - "scored-vcf-clinical-index", - "T-panel", - "vcf-clinical", - "merged" + "namemap-snv", + "research-namemap-snv" ], "id": "T-panel", - "format": "vcf.gz.tbi" + "format": "sample_name_map" }, { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.tnscope_umi.clinical.scored.vcf.gz", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SV.somatic.T-panel.svdb.clinical.filtered.pass.vcf.gz", "path_index": [ - "T-panel/analysis/vep/SNV.somatic.T-panel.tnscope_umi.clinical.scored.vcf.gz.tbi" + "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SV.somatic.T-panel.svdb.clinical.filtered.pass.vcf.gz.tbi" ], - "step": "genmod_score_snvs", + "step": "bcftools_filter_sv_clinical", "tag": [ - "SNV", + "vcf-pass-svdb", "T-panel", - "vcf-clinical", - "scored-vcf-clinical", - "tnscope-umi" + "clinical-vcf-pass-svdb" ], "id": "T-panel", "format": "vcf.gz" }, { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.tnscope_umi.clinical.scored.vcf.gz.tbi", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SV.somatic.T-panel.svdb.clinical.filtered.pass.vcf.gz.tbi", "path_index": "", - "step": "genmod_score_snvs", + "step": "bcftools_filter_sv_clinical", "tag": [ - "SNV", - "scored-vcf-clinical-index", - "T-panel", - "vcf-clinical", - "tnscope-umi" + "vcf-pass-svdb", + "clinical-vcf-pass-svdb-index", + "T-panel" ], "id": "T-panel", "format": "vcf.gz.tbi" }, { - "path": "T-panel/analysis/vcf/CNV.somatic.T-panel.cnvkit.vcf2cytosure.cgh", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SV.somatic.T-panel.svdb.clinical.filtered.pass.stats", "path_index": [], - "step": "vcf2cytosure_convert", + "step": "bcftools_filter_sv_clinical", "tag": [ - "cgh-tumor", - "cnv-somatic-cgh-tumor" + "bcftools-counts", + "clinical-bcftools-counts", + "T-panel" ], "id": "T-panel", - "format": "cgh" + "format": "stats" }, { - "path": "T-panel/analysis/cnv/CNV.somatic.T-panel.report.pdf", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_report.html", "path_index": [], - "step": "merge_cnv_pdf_reports", - "tag": [ - "clinical-cnv-report-pdf", - "cnv-report-pdf" - ], - "id": "T-panel", - "format": "pdf" - }, - { - "path": "T-panel/analysis/vcf/SNV.somatic.T-panel.tnscope_umi.vcf.gz", - "path_index": [ - "T-panel/analysis/vcf/SNV.somatic.T-panel.tnscope_umi.vcf.gz.tbi" - ], - "step": "modify_tnscope_infofield_umi", - "tag": [ - "research-vcf-tnscope-umi", - "vcf-tnscope-umi" - ], - "id": "T-panel", - "format": "vcf.gz" - }, - { - "path": "T-panel/analysis/vcf/SNV.somatic.T-panel.tnscope_umi.vcf.gz.tbi", - "path_index": "", - "step": "modify_tnscope_infofield_umi", - "tag": [ - "research-vcf-tnscope-umi-index", - "vcf-tnscope-umi" - ], - "id": "T-panel", - "format": "vcf.gz.tbi" - }, - { - "path": "T-panel/analysis/vep/SV.somatic.T-panel.svdb.clinical.filtered.pass.vcf.gz", - "path_index": [ - "T-panel/analysis/vep/SV.somatic.T-panel.svdb.clinical.filtered.pass.vcf.gz.tbi" - ], - "step": "bcftools_filter_sv_clinical", + "step": "multiqc", "tag": [ - "clinical-vcf-pass-svdb", - "T-panel", - "vcf-pass-svdb" + "multiqc-html", + "html" ], "id": "T-panel", - "format": "vcf.gz" + "format": "html" }, { - "path": "T-panel/analysis/vep/SV.somatic.T-panel.svdb.clinical.filtered.pass.vcf.gz.tbi", - "path_index": "", - "step": "bcftools_filter_sv_clinical", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/multiqc_data.json", + "path_index": [], + "step": "multiqc", "tag": [ - "T-panel", - "clinical-vcf-pass-svdb-index", - "vcf-pass-svdb" + "json", + "multiqc-json" ], "id": "T-panel", - "format": "vcf.gz.tbi" + "format": "json" }, { - "path": "T-panel/analysis/vep/SV.somatic.T-panel.svdb.clinical.filtered.pass.stats", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.somatic.T-panel.merged.balsamic_stat", "path_index": [], - "step": "bcftools_filter_sv_clinical", + "step": "tmb_calculation", "tag": [ + "SNV", + "tmb", "T-panel", - "clinical-bcftools-counts", - "bcftools-counts" + "research-tmb", + "merged" ], "id": "T-panel", - "format": "stats" + "format": "balsamic_stat" }, { - "path": "T-panel/analysis/cnv/tumorsample.baf.bed.gz", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/cnv/tumorsample.cov.bed.gz", "path_index": [ - "T-panel/analysis/cnv/tumorsample.baf.bed.gz.tbi" + "/home/proj/stage/cancer/cases/T-panel/analysis/cnv/tumorsample.cov.bed.gz.tbi" ], "step": "finalize_gens_outputfiles", "tag": [ + "cov", "cnv-gens-bed", "tumorsample", - "baf", "gens-bed" ], "id": "tumorsample", "format": "gz" }, { - "path": "T-panel/analysis/cnv/tumorsample.baf.bed.gz.tbi", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/cnv/tumorsample.cov.bed.gz.tbi", "path_index": "", "step": "finalize_gens_outputfiles", "tag": [ + "cov", "tumorsample", - "baf", "gens-bed", "cnv-gens-bed-index" ], @@ -568,27 +243,27 @@ "format": "tbi" }, { - "path": "T-panel/analysis/cnv/tumorsample.cov.bed.gz", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/cnv/tumorsample.baf.bed.gz", "path_index": [ - "T-panel/analysis/cnv/tumorsample.cov.bed.gz.tbi" + "/home/proj/stage/cancer/cases/T-panel/analysis/cnv/tumorsample.baf.bed.gz.tbi" ], "step": "finalize_gens_outputfiles", "tag": [ + "baf", "cnv-gens-bed", "tumorsample", - "cov", "gens-bed" ], "id": "tumorsample", "format": "gz" }, { - "path": "T-panel/analysis/cnv/tumorsample.cov.bed.gz.tbi", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/cnv/tumorsample.baf.bed.gz.tbi", "path_index": "", "step": "finalize_gens_outputfiles", "tag": [ + "baf", "tumorsample", - "cov", "gens-bed", "cnv-gens-bed-index" ], @@ -596,212 +271,216 @@ "format": "tbi" }, { - "path": "T-panel/analysis/qc/multiqc_report.html", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/cnv/tumor.merged.cns", "path_index": [], - "step": "multiqc", + "step": "cnvkit_call_CNV_research", "tag": [ - "multiqc-html", - "html" + "cnv-cns", + "cns" ], "id": "T-panel", - "format": "html" + "format": "cns" }, { - "path": "T-panel/analysis/qc/multiqc_data/multiqc_data.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/cnv/T-panel.gene_breaks", "path_index": [], - "step": "multiqc", + "step": "cnvkit_call_CNV_research", "tag": [ - "multiqc-json", - "json" + "cnv-gene-breaks", + "gene-breaks" ], "id": "T-panel", - "format": "json" + "format": "gene_breaks" }, { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.merged.research.filtered.pass.vcf.gz", - "path_index": [ - "T-panel/analysis/vep/SNV.somatic.T-panel.merged.research.filtered.pass.vcf.gz.tbi" - ], - "step": "bcftools_filter_merged_research_tumor_only", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/cnv/T-panel.gene_metrics", + "path_index": [], + "step": "cnvkit_call_CNV_research", "tag": [ - "research-vcf-pass-merged", - "SNV", - "T-panel", - "vcf-pass-merged" + "gene-metrics", + "cnv-gene-metrics" ], "id": "T-panel", - "format": "vcf.gz" + "format": "gene_metrics" }, { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.merged.research.filtered.pass.vcf.gz.tbi", - "path_index": "", - "step": "bcftools_filter_merged_research_tumor_only", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/cnv/CNV.somatic.T-panel.cnvkit.vcf", + "path_index": [], + "step": "cnvkit_call_CNV_research", "tag": [ - "research-vcf-pass-merged-index", - "SNV", - "T-panel", - "vcf-pass-merged" + "vcf", + "cnv-vcf" ], "id": "T-panel", - "format": "vcf.gz.tbi" + "format": "vcf" }, { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.merged.research.filtered.pass.stats", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/cnv/tumor.merged-diagram.pdf", "path_index": [], - "step": "bcftools_filter_merged_research_tumor_only", + "step": "cnvkit_call_CNV_research", "tag": [ - "SNV", - "T-panel", - "research-bcftools-counts-research", - "bcftools-counts-research" + "diagram", + "cnv-diagram" ], "id": "T-panel", - "format": "stats" + "format": "pdf" }, { - "path": "T-panel/analysis/cnv/tumor.initial.cns", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/cnv/tumor.merged-scatter.pdf", "path_index": [], - "step": "cnvkit_segment_CNV_research", + "step": "cnvkit_call_CNV_research", "tag": [ - "cnv-cns-initial", - "cns-initial" + "cnv-scatter", + "scatter" ], "id": "T-panel", - "format": "cns" + "format": "pdf" }, { - "path": "T-panel/analysis/cnv/tumor.merged.cnr", - "path_index": [], - "step": "cnvkit_segment_CNV_research", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SV.germline.tumor.manta_germline.vcf.gz", + "path_index": [ + "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SV.germline.tumor.manta_germline.vcf.gz.tbi" + ], + "step": "vep_annotate_germlineVAR_tumor", "tag": [ - "cnr", - "cnv-cnr" + "vcf-tumor", + "SV", + "manta-germline", + "germline-vcf-tumor" ], "id": "T-panel", - "format": "cnr" + "format": "vcf.gz" }, { - "path": "T-panel/analysis/cnv/tumor.seg", - "path_index": [], - "step": "cnvkit_segment_CNV_research", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SV.germline.tumor.manta_germline.vcf.gz.tbi", + "path_index": "", + "step": "vep_annotate_germlineVAR_tumor", "tag": [ - "cnv-segment", - "segment" + "vcf-tumor", + "SV", + "germline-vcf-tumor-index", + "manta-germline" ], "id": "T-panel", - "format": "seg" + "format": "vcf.gz.tbi" }, { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.tnscope_umi.clinical.filtered.pass.vcf.gz", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.germline.tumor.dnascope.vcf.gz", "path_index": [ - "T-panel/analysis/vep/SNV.somatic.T-panel.tnscope_umi.clinical.filtered.pass.vcf.gz.tbi" + "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.germline.tumor.dnascope.vcf.gz.tbi" ], - "step": "bcftools_filter_TNscope_umi_clinical_tumor_only", + "step": "vep_annotate_germlineVAR_tumor", "tag": [ - "clinical-vcf-pass-tnscope-umi", + "dnascope", + "vcf-tumor", "SNV", - "T-panel", - "vcf-pass-tnscope-umi" + "germline-vcf-tumor" ], "id": "T-panel", "format": "vcf.gz" }, { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.tnscope_umi.clinical.filtered.pass.vcf.gz.tbi", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.germline.tumor.dnascope.vcf.gz.tbi", "path_index": "", - "step": "bcftools_filter_TNscope_umi_clinical_tumor_only", + "step": "vep_annotate_germlineVAR_tumor", + "tag": [ + "dnascope", + "vcf-tumor", + "germline-vcf-tumor-index", + "SNV" + ], + "id": "T-panel", + "format": "vcf.gz.tbi" + }, + { + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.somatic.T-panel.merged.clinical.scored.vcf.gz", + "path_index": [ + "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.somatic.T-panel.merged.clinical.scored.vcf.gz.tbi" + ], + "step": "genmod_score_snvs", "tag": [ "SNV", + "scored-vcf-clinical", "T-panel", - "vcf-pass-tnscope-umi", - "clinical-vcf-pass-tnscope-umi-index" + "vcf-clinical", + "merged" ], "id": "T-panel", - "format": "vcf.gz.tbi" + "format": "vcf.gz" }, { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.tnscope_umi.clinical.filtered.pass.stats", - "path_index": [], - "step": "bcftools_filter_TNscope_umi_clinical_tumor_only", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.somatic.T-panel.merged.clinical.scored.vcf.gz.tbi", + "path_index": "", + "step": "genmod_score_snvs", "tag": [ - "bcftools-counts-clinical", + "scored-vcf-clinical-index", "SNV", "T-panel", - "clinical-bcftools-counts-clinical" + "vcf-clinical", + "merged" ], "id": "T-panel", - "format": "stats" + "format": "vcf.gz.tbi" }, { - "path": "T-panel/analysis/vcf/SNV.somatic.T-panel.tnscope.vcf.gz", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vcf/SNV.somatic.T-panel.vardict.vcf.gz", "path_index": [ - "T-panel/analysis/vcf/SNV.somatic.T-panel.tnscope.vcf.gz.tbi" + "/home/proj/stage/cancer/cases/T-panel/analysis/vcf/SNV.somatic.T-panel.vardict.vcf.gz.tbi" ], - "step": "modify_tnscope_infofield", + "step": "gatk_update_vcf_sequence_dictionary", "tag": [ - "vcf-tnscope", - "research-vcf-tnscope" + "research-vcf-vardict", + "vcf-vardict" ], "id": "T-panel", "format": "vcf.gz" }, { - "path": "T-panel/analysis/vcf/SNV.somatic.T-panel.tnscope.vcf.gz.tbi", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vcf/SNV.somatic.T-panel.vardict.vcf.gz.tbi", "path_index": "", - "step": "modify_tnscope_infofield", + "step": "gatk_update_vcf_sequence_dictionary", "tag": [ - "vcf-tnscope", - "research-vcf-tnscope-index" + "research-vcf-vardict-index", + "vcf-vardict" ], "id": "T-panel", "format": "vcf.gz.tbi" }, { - "path": "T-panel/analysis/qc/T-panel_metrics_deliverables.yaml", - "path_index": [], - "step": "collect_custom_qc_metrics", - "tag": [ - "yaml", - "qc-metrics-yaml" - ], - "id": "T-panel", - "format": "yaml" - }, - { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.merged.clinical.filtered.pass.vcf.gz", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.somatic.T-panel.merged.clinical.filtered.pass.vcf.gz", "path_index": [ - "T-panel/analysis/vep/SNV.somatic.T-panel.merged.clinical.filtered.pass.vcf.gz.tbi" + "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.somatic.T-panel.merged.clinical.filtered.pass.vcf.gz.tbi" ], "step": "bcftools_filter_merged_clinical_tumor_only", "tag": [ - "SNV", - "T-panel", "vcf-pass-merged", - "clinical-vcf-pass-merged" + "clinical-vcf-pass-merged", + "SNV", + "T-panel" ], "id": "T-panel", "format": "vcf.gz" }, { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.merged.clinical.filtered.pass.vcf.gz.tbi", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.somatic.T-panel.merged.clinical.filtered.pass.vcf.gz.tbi", "path_index": "", "step": "bcftools_filter_merged_clinical_tumor_only", "tag": [ + "vcf-pass-merged", "SNV", - "T-panel", "clinical-vcf-pass-merged-index", - "vcf-pass-merged" + "T-panel" ], "id": "T-panel", "format": "vcf.gz.tbi" }, { - "path": "T-panel/analysis/vep/SNV.somatic.T-panel.merged.clinical.filtered.pass.stats", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.somatic.T-panel.merged.clinical.filtered.pass.stats", "path_index": [], "step": "bcftools_filter_merged_clinical_tumor_only", "tag": [ - "bcftools-counts-clinical", "SNV", + "bcftools-counts-clinical", "T-panel", "clinical-bcftools-counts-clinical" ], @@ -809,71 +488,181 @@ "format": "stats" }, { - "path": "T-panel/analysis/vep/SV.somatic.T-panel.svdb.research.filtered.pass.vcf.gz", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vcf/CNV.somatic.T-panel.cnvkit.vcf2cytosure.cgh", + "path_index": [], + "step": "vcf2cytosure_convert", + "tag": [ + "cnv-somatic-cgh-tumor", + "cgh-tumor" + ], + "id": "T-panel", + "format": "cgh" + }, + { + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/T-panel_metrics_deliverables.yaml", + "path_index": [], + "step": "collect_custom_qc_metrics", + "tag": [ + "qc-metrics-yaml", + "yaml" + ], + "id": "T-panel", + "format": "yaml" + }, + { + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/tumor.tumorsample.d4", + "path_index": [], + "step": "create_d4file", + "tag": [ + "d4file", + "tumorsample", + "qc-metrics-d4file" + ], + "id": "T-panel", + "format": "d4" + }, + { + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SV.somatic.T-panel.svdb.research.filtered.pass.vcf.gz", "path_index": [ - "T-panel/analysis/vep/SV.somatic.T-panel.svdb.research.filtered.pass.vcf.gz.tbi" + "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SV.somatic.T-panel.svdb.research.filtered.pass.vcf.gz.tbi" ], "step": "bcftools_filter_sv_research", "tag": [ + "vcf-pass-svdb", "research-vcf-pass-svdb", - "T-panel", - "vcf-pass-svdb" + "T-panel" ], "id": "T-panel", "format": "vcf.gz" }, { - "path": "T-panel/analysis/vep/SV.somatic.T-panel.svdb.research.filtered.pass.vcf.gz.tbi", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SV.somatic.T-panel.svdb.research.filtered.pass.vcf.gz.tbi", "path_index": "", "step": "bcftools_filter_sv_research", "tag": [ - "T-panel", + "vcf-pass-svdb", "research-vcf-pass-svdb-index", - "vcf-pass-svdb" + "T-panel" ], "id": "T-panel", "format": "vcf.gz.tbi" }, { - "path": "T-panel/analysis/vep/SV.somatic.T-panel.svdb.research.filtered.pass.stats", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SV.somatic.T-panel.svdb.research.filtered.pass.stats", "path_index": [], "step": "bcftools_filter_sv_research", "tag": [ - "T-panel", "bcftools-counts", - "research-bcftools-counts" + "research-bcftools-counts", + "T-panel" ], "id": "T-panel", "format": "stats" }, { - "path": "T-panel/analysis/umi/tumor.tumorsample.consensusfiltered_umi.cram", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.somatic.T-panel.merged.cadd_indel.research.vcf.gz", "path_index": [ - "T-panel/analysis/umi/tumor.tumorsample.consensusfiltered_umi.cram.crai" + "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.somatic.T-panel.merged.cadd_indel.research.vcf.gz.tbi" ], - "step": "bam_compress_tumor_umi", + "step": "vep_annotate_somaticSNV_research", "tag": [ - "umi-tumor-cram", - "cram", - "tumorsample" + "cadd-indel", + "research-vcf-snv-unfiltered", + "vcf-snv-unfiltered", + "T-panel.merged" ], - "id": "tumorsample", - "format": "cram" + "id": "T-panel", + "format": "vcf.gz" }, { - "path": "T-panel/analysis/umi/tumor.tumorsample.consensusfiltered_umi.cram.crai", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.somatic.T-panel.merged.cadd_indel.research.vcf.gz.tbi", "path_index": "", - "step": "bam_compress_tumor_umi", + "step": "vep_annotate_somaticSNV_research", "tag": [ - "cram", - "tumorsample", - "umi-tumor-cram-index" + "cadd-indel", + "research-vcf-snv-unfiltered-index", + "vcf-snv-unfiltered", + "T-panel.merged" ], - "id": "tumorsample", - "format": "crai" + "id": "T-panel", + "format": "vcf.gz.tbi" + }, + { + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.somatic.T-panel.merged.research.vcf.gz", + "path_index": [ + "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.somatic.T-panel.merged.research.vcf.gz.tbi" + ], + "step": "vep_annotate_somaticSNV_research", + "tag": [ + "research-vcf-snv-unfiltered", + "merged", + "vcf-snv-unfiltered", + "T-panel" + ], + "id": "T-panel", + "format": "vcf.gz" + }, + { + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.somatic.T-panel.merged.research.vcf.gz.tbi", + "path_index": "", + "step": "vep_annotate_somaticSNV_research", + "tag": [ + "research-vcf-snv-unfiltered-index", + "merged", + "vcf-snv-unfiltered", + "T-panel" + ], + "id": "T-panel", + "format": "vcf.gz.tbi" + }, + { + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/vep/SNV.somatic.T-panel.merged_vcfanno_research.toml", + "path_index": [], + "step": "vep_annotate_somaticSNV_research", + "tag": [ + "research-vcfanno-research-toml", + "vcfanno-research-toml", + "merged", + "T-panel" + ], + "id": "T-panel", + "format": "toml" + }, + { + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/cnv/tumor.initial.cns", + "path_index": [], + "step": "cnvkit_segment_CNV_research", + "tag": [ + "cnv-cns-initial", + "cns-initial" + ], + "id": "T-panel", + "format": "cns" + }, + { + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/cnv/tumor.merged.cnr", + "path_index": [], + "step": "cnvkit_segment_CNV_research", + "tag": [ + "cnr", + "cnv-cnr" + ], + "id": "T-panel", + "format": "cnr" + }, + { + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/cnv/tumor.seg", + "path_index": [], + "step": "cnvkit_segment_CNV_research", + "tag": [ + "cnv-segment", + "segment" + ], + "id": "T-panel", + "format": "seg" }, { - "path": "T-panel/T-panel.json", + "path": "/home/proj/stage/cancer/cases/T-panel/T-panel.json", "step": "case_config", "format": "json", "tag": [ @@ -882,7 +671,7 @@ "id": "T-panel" }, { - "path": "T-panel/T-panel_BALSAMIC_15.0.1_graph.pdf", + "path": "/home/proj/stage/cancer/cases/T-panel/T-panel_BALSAMIC_17.0.1_graph.pdf", "step": "case_config", "format": "pdf", "tag": [ @@ -891,7 +680,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.json", "step": "multiqc", "format": "json", "tag": [ @@ -902,7 +691,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.json", "step": "multiqc", "format": "json", "tag": [ @@ -915,7 +704,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastp-seq-quality-plot_Read_2_Before_filtering.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastp-seq-quality-plot_Read_2_Before_filtering.json", "step": "multiqc", "format": "json", "tag": [ @@ -928,7 +717,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastp-seq-quality-plot_Read_2_After_filtering.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastp-seq-quality-plot_Read_2_After_filtering.json", "step": "multiqc", "format": "json", "tag": [ @@ -941,7 +730,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/samtools-idxstats-xy-plot.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/samtools-idxstats-xy-plot.json", "step": "multiqc", "format": "json", "tag": [ @@ -950,7 +739,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/mosdepth-cumcoverage-dist-id.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/mosdepth-cumcoverage-dist-id.json", "step": "multiqc", "format": "json", "tag": [ @@ -959,7 +748,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/mosdepth-xy-coverage-plot.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/mosdepth-xy-coverage-plot.json", "step": "multiqc", "format": "json", "tag": [ @@ -968,7 +757,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastqc_per_sequence_quality_scores_plot.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastqc_per_sequence_quality_scores_plot.json", "step": "multiqc", "format": "json", "tag": [ @@ -982,7 +771,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/picard_hybrid_selection_penalty.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/picard_hybrid_selection_penalty.json", "step": "multiqc", "format": "json", "tag": [ @@ -994,7 +783,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastqc_per_base_sequence_quality_plot.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastqc_per_base_sequence_quality_plot.json", "step": "multiqc", "format": "json", "tag": [ @@ -1008,7 +797,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastp_filtered_reads_plot.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastp_filtered_reads_plot.json", "step": "multiqc", "format": "json", "tag": [ @@ -1020,7 +809,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/picard_deduplication.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/picard_deduplication.json", "step": "multiqc", "format": "json", "tag": [ @@ -1030,7 +819,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/multiqc_citations.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/multiqc_citations.json", "step": "multiqc", "format": "json", "tag": [ @@ -1040,7 +829,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastqc_sequence_counts_plot.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastqc_sequence_counts_plot.json", "step": "multiqc", "format": "json", "tag": [ @@ -1052,7 +841,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/picard_percentage_target_bases.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/picard_percentage_target_bases.json", "step": "multiqc", "format": "json", "tag": [ @@ -1064,7 +853,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.json", "step": "multiqc", "format": "json", "tag": [ @@ -1075,7 +864,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/mosdepth-coverage-per-contig-multi.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/mosdepth-coverage-per-contig-multi.json", "step": "multiqc", "format": "json", "tag": [ @@ -1084,7 +873,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/multiqc_data.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/multiqc_data.json", "step": "multiqc", "format": "json", "tag": [ @@ -1094,7 +883,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/samtools_alignment_plot.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/samtools_alignment_plot.json", "step": "multiqc", "format": "json", "tag": [ @@ -1105,7 +894,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.json", "step": "multiqc", "format": "json", "tag": [ @@ -1118,7 +907,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/picard_hsmetrics_table.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/picard_hsmetrics_table.json", "step": "multiqc", "format": "json", "tag": [ @@ -1129,7 +918,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/picard_alignment_summary_Aligned_Reads.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/picard_alignment_summary_Aligned_Reads.json", "step": "multiqc", "format": "json", "tag": [ @@ -1142,7 +931,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/samtools-flagstat-dp_Percentage_of_total.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/samtools-flagstat-dp_Percentage_of_total.json", "step": "multiqc", "format": "json", "tag": [ @@ -1154,7 +943,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.json", "step": "multiqc", "format": "json", "tag": [ @@ -1169,7 +958,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastqc_adapter_content_plot.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastqc_adapter_content_plot.json", "step": "multiqc", "format": "json", "tag": [ @@ -1181,7 +970,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.json", "step": "multiqc", "format": "json", "tag": [ @@ -1194,7 +983,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.json", "step": "multiqc", "format": "json", "tag": [ @@ -1207,7 +996,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/picard_alignment_summary_Aligned_Bases.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/picard_alignment_summary_Aligned_Bases.json", "step": "multiqc", "format": "json", "tag": [ @@ -1220,7 +1009,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/multiqc_general_stats.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/multiqc_general_stats.json", "step": "multiqc", "format": "json", "tag": [ @@ -1231,7 +1020,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastp-insert-size-plot.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastp-insert-size-plot.json", "step": "multiqc", "format": "json", "tag": [ @@ -1240,7 +1029,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/picard_quality_by_cycle.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/picard_quality_by_cycle.json", "step": "multiqc", "format": "json", "tag": [ @@ -1252,7 +1041,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.json", "step": "multiqc", "format": "json", "tag": [ @@ -1265,7 +1054,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.json", "step": "multiqc", "format": "json", "tag": [ @@ -1278,18 +1067,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/picard_gcbias_plot.json", - "step": "multiqc", - "format": "json", - "tag": [ - "picard", - "gcbias", - "plot" - ], - "id": "T-panel" - }, - { - "path": "T-panel/analysis/qc/multiqc_data/fastp-seq-content-gc-plot_Read_2_After_filtering.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastp-seq-content-gc-plot_Read_2_After_filtering.json", "step": "multiqc", "format": "json", "tag": [ @@ -1302,7 +1080,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastp-seq-content-n-plot_Read_2_After_filtering.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastp-seq-content-n-plot_Read_2_After_filtering.json", "step": "multiqc", "format": "json", "tag": [ @@ -1315,7 +1093,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastp-seq-content-gc-plot_Read_2_Before_filtering.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastp-seq-content-gc-plot_Read_2_Before_filtering.json", "step": "multiqc", "format": "json", "tag": [ @@ -1328,7 +1106,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/picard_quality_score_distribution.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/picard_quality_score_distribution.json", "step": "multiqc", "format": "json", "tag": [ @@ -1340,7 +1118,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastqc-status-check-heatmap.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastqc-status-check-heatmap.json", "step": "multiqc", "format": "json", "tag": [ @@ -1349,7 +1127,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/multiqc_sources.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/multiqc_sources.json", "step": "multiqc", "format": "json", "tag": [ @@ -1359,7 +1137,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/picard_alignment_readlength_plot.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/picard_alignment_readlength_plot.json", "step": "multiqc", "format": "json", "tag": [ @@ -1371,7 +1149,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastqc_sequence_duplication_levels_plot.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastqc_sequence_duplication_levels_plot.json", "step": "multiqc", "format": "json", "tag": [ @@ -1384,7 +1162,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/mosdepth-coverage-dist-id.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/mosdepth-coverage-dist-id.json", "step": "multiqc", "format": "json", "tag": [ @@ -1393,7 +1171,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/samtools-flagstat-dp_Read_counts.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/samtools-flagstat-dp_Read_counts.json", "step": "multiqc", "format": "json", "tag": [ @@ -1404,7 +1182,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastp-seq-content-n-plot_Read_2_Before_filtering.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastp-seq-content-n-plot_Read_2_Before_filtering.json", "step": "multiqc", "format": "json", "tag": [ @@ -1417,7 +1195,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/samtools-stats-dp.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/samtools-stats-dp.json", "step": "multiqc", "format": "json", "tag": [ @@ -1426,7 +1204,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastqc_top_overrepresented_sequences_table.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastqc_top_overrepresented_sequences_table.json", "step": "multiqc", "format": "json", "tag": [ @@ -1439,7 +1217,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.json", "step": "multiqc", "format": "json", "tag": [ @@ -1454,7 +1232,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastqc_per_base_n_content_plot.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastqc_per_base_n_content_plot.json", "step": "multiqc", "format": "json", "tag": [ @@ -1468,7 +1246,7 @@ "id": "T-panel" }, { - "path": "T-panel/analysis/qc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.json", + "path": "/home/proj/stage/cancer/cases/T-panel/analysis/qc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.json", "step": "multiqc", "format": "json", "tag": [ @@ -1480,5 +1258,4 @@ ], "id": "T-panel" } - ] -} \ No newline at end of file + ] \ No newline at end of file