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| - format: bam | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/aligned_reads/SAMPLENAME/SAMPLENAME_haplotagged.bam | ||
| path_index: ~ | ||
| step: alignment | ||
| tag: alignment_haplotags | ||
| - format: bam | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/aligned_reads/SAMPLENAME/SAMPLENAME_haplotagged.bam.bai | ||
| path_index: ~ | ||
| step: alignment | ||
| tag: alignment_haplotags_index | ||
| - format: txt | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/assembly_haplotypes/gfastats/SAMPLENAME/SAMPLENAME.asm.bp.hap1.p_ctg.assembly_summary | ||
| path_index: ~ | ||
| step: assembly | ||
| tag: summary_hap1 | ||
| - format: txt | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/assembly_haplotypes/gfastats/SAMPLENAME/SAMPLENAME.asm.bp.hap2.p_ctg.assembly_summary | ||
| path_index: ~ | ||
| step: assembly | ||
| tag: summary_hap1 | ||
| - format: bam | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/assembly_variant_calling/dipcall/SAMPLENAME/SAMPLENAME.hap1.bam | ||
| path_index: ~ | ||
| step: assembly | ||
| tag: assembly_hap1_mapped | ||
| - format: bam | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/assembly_variant_calling/dipcall/SAMPLENAME/SAMPLENAME.hap1.bam.bai | ||
| path_index: ~ | ||
| step: assembly | ||
| tag: assembly_hap1_mapped_index | ||
| - format: bam | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/assembly_variant_calling/dipcall/SAMPLENAME/SAMPLENAME.hap2.bam | ||
| path_index: ~ | ||
| step: assembly | ||
| tag: assembly_hap2_mapped | ||
| - format: bam | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/assembly_variant_calling/dipcall/SAMPLENAME/SAMPLENAME.hap2.bam.bai | ||
| path_index: ~ | ||
| step: assembly | ||
| tag: assembly_hap2_mapped_index | ||
| - format: bed | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/methylation/modkit/pileup/SAMPLENAME/SAMPLENAME_modkit_pileup_1.bed.gz | ||
| path_index: ~ | ||
| step: summary_counts | ||
| tag: hap1 | ||
| - format: bed | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/methylation/modkit/pileup/SAMPLENAME/SAMPLENAME_modkit_pileup_1.bed.gz/tbi | ||
| path_index: ~ | ||
| step: summary_counts | ||
| tag: hap1_index | ||
| - format: bed | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/methylation/modkit/pileup/SAMPLENAME/SAMPLENAME_modkit_pileup_2.bed.gz | ||
| path_index: ~ | ||
| step: summary_counts | ||
| tag: hap2 | ||
| - format: bed | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/methylation/modkit/pileup/SAMPLENAME/SAMPLENAME_modkit_pileup_2.bed.gz/tbi | ||
| path_index: ~ | ||
| step: summary_counts | ||
| tag: hap2_index | ||
| - format: bed | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/methylation/modkit/pileup/SAMPLENAME/SAMPLENAME_modkit_pileup_2.bed.gz | ||
| path_index: ~ | ||
| step: summary_counts | ||
| tag: ungrouped | ||
| - format: bed | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/methylation/modkit/pileup/SAMPLENAME/SAMPLENAME_modkit_pileup_ungrouped.bed.gz/tbi | ||
| path_index: ~ | ||
| step: summary_counts | ||
| tag: ungrouped_index | ||
| - format: d4 | ||
| id: SAMPLEID | ||
| path: PATHTOCASE/qc_bam/SAMPLEID_mosdepth.per-base.d4 | ||
| path_index: ~ | ||
| step: qc_bam | ||
| tag: mosdepth_d4 | ||
| - format: meta | ||
| id: CASEID | ||
| path: PATHTOCASE/pedigree/CASEID.ped | ||
| path_index: ~ | ||
| step: pedigree | ||
| tag: pedigree_fam | ||
| - format: html | ||
| id: CASEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/qc/somalier/relate/CASEID/CASEID.html | ||
| path_index: ~ | ||
| step: somalier | ||
| tag: relate_html | ||
| - format: tsv | ||
| id: CASEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/qc/somalier/relate/CASEID/CASEID.pairs.tsv | ||
| path_index: ~ | ||
| step: somalier | ||
| tag: relate_pairs | ||
| - format: tsv | ||
| id: CASEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/qc/somalier/relate/CASEID/CASEID.samples.tsv | ||
| path_index: ~ | ||
| step: somalier | ||
| tag: relate_samples | ||
| - format: html | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/qc/deepvariant_vcfstatsreport/SAMPLENAME/SAMPLENAME.visual_report.html | ||
| path_index: ~ | ||
| step: deepvariant | ||
| tag: report | ||
| - format: bam | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/paraphase/SAMPLENAME/SAMPLENAME.paraphase.bam | ||
| path_index: ~ | ||
| step: paraphase | ||
| tag: paraphase | ||
| - format: bam | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/paraphase/SAMPLENAME/SAMPLENAME.paraphase.bam.bai | ||
| path_index: ~ | ||
| step: paraphase | ||
| tag: paraphase_index | ||
| - format: json | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/paraphase/SAMPLENAME/SAMPLENAME.paraphase.json | ||
| path_index: ~ | ||
| step: paraphase | ||
| tag: json | ||
| - format: vcf | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/paraphase/SAMPLENAME/SAMPLENAME_paraphase_vcfs/SAMPLENAME_*.vcf.gz | ||
| path_index: ~ | ||
| step: paraphase | ||
| tag: vcf | ||
| - format: vcf | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/paraphase/SAMPLENAME/SAMPLENAME_paraphase_vcfs/SAMPLENAME_*.vcf.gz.tbi | ||
| path_index: ~ | ||
| step: paraphase | ||
| tag: vcf_index | ||
| - format: vcf | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/repeats/sample/SAMPLENAME/SAMPLENAME_sorted.vcf.gz | ||
| path_index: ~ | ||
| step: sorted_repeats | ||
| tag: vcf_str | ||
| - format: vcf | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/repeats/sample/SAMPLENAME/SAMPLENAME_sorted.vcf.gz.tbi | ||
| path_index: ~ | ||
| step: sorted_repeats | ||
| tag: vcf_str_index | ||
| - format: vcf | ||
| id: CASEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/snvs/family/CASEID/CASEID_snv_annotated_ranked.vcf.gz | ||
| path_index: ~ | ||
| step: snv_annotated | ||
| tag: vcf_snv_research | ||
| - format: vcf | ||
| id: CASEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/snvs/family/CASEID/CASEID_snv_annotated_ranked.vcf.gz.tbi | ||
| path_index: ~ | ||
| step: snv_annotated | ||
| tag: vcf_snv_research_index | ||
| - format: vcf | ||
| id: CASEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/snvs/family/CASEID/CASEID_snvs_annotated_ranked_filtered.vcf.gz | ||
| path_index: ~ | ||
| step: snv_annotated_filtered | ||
| tag: vcf_snv_clinical | ||
| - format: vcf | ||
| id: CASEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/snvs/family/CASEID/CASEID_snvs_annotated_ranked_filtered.vcf.gz.tbi | ||
| path_index: ~ | ||
| step: snv_annotated_filtered | ||
| tag: vcf_snv_clinical_index | ||
| - format: vcf | ||
| id: CASEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/snvs/family/CASEID/CASEID_snvs_annotated_ranked_filtered.vcf.gz | ||
| path_index: ~ | ||
| step: snv_annotated_filtered | ||
| tag: vcf_snv_clinical | ||
| - format: vcf | ||
| id: CASEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/snvs/family/CASEID/CASEID_snvs_annotated_ranked_filtered.vcf.gz.tbi | ||
| path_index: ~ | ||
| step: snv_annotated_filtered | ||
| tag: vcf_snv_clinical_index | ||
| - format: vcf | ||
| id: CASEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/svs/family/CASEID/CASEID_svs_cnvs_merged_annotated_ranked.vcf.gz | ||
| path_index: ~ | ||
| step: sv_annotated_ranked | ||
| tag: vcf_sv_research | ||
| - format: vcf | ||
| id: CASEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/svs/family/CASEID/CASEID_svs_cnvs_merged_annotated_ranked.vcf.gz.tbi | ||
| path_index: ~ | ||
| step: sv_annotated_ranked | ||
| tag: vcf_sv_research_index | ||
| - format: vcf | ||
| id: CASEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/svs/family/CASEID/CASEID_svs_cnvs_merged_annotated_ranked_filtered.vcf.gz | ||
| path_index: ~ | ||
| step: sv_annotated_ranked_filtered | ||
| tag: vcf_sv_clinical | ||
| - format: vcf | ||
| id: CASEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/svs/family/CASEID/CASEID_svs_cnvs_merged_annotated_ranked_filtered.vcf.gz.tbi | ||
| path_index: ~ | ||
| step: sv_annotated_ranked_filtered | ||
| tag: vcf_sv_clinical_index | ||
| - format: meta | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/visualization_tracks/SAMPLENAME/SAMPLENAME_hificnv.copynum.bedgraph | ||
| path_index: ~ | ||
| step: copy_number | ||
| tag: bedgraph | ||
| - format: bw | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/visualization_tracks/SAMPLENAME/SAMPLENAME_hificnv.depth.bw | ||
| path_index: ~ | ||
| step: depth_track | ||
| tag: bigwig | ||
| - format: bw | ||
| id: SAMPLEID | ||
| path: /home/proj/stage/analysis/cases/CASEID/visualization_tracks/SAMPLENAME/SAMPLENAME_hificnv.maf.bw | ||
| path_index: ~ | ||
| step: maf_depth_track | ||
| tag: bigwig | ||
| - format: meta | ||
| id: CASEID | ||
| path: PATHTOCASE/multiqc/multiqc_data/multiqc_data.json | ||
| path_index: ~ | ||
| step: multiqc | ||
| tag: multiqc-json | ||
| - format: meta | ||
| id: CASEID | ||
| path: PATHTOCASE/multiqc/multiqc_report.html | ||
| path_index: ~ | ||
| step: multiqc | ||
| tag: multiqc-html | ||
| - format: csv | ||
| id: CASEID | ||
| path: PATHTOCASE/CASEID_samplesheet.csv | ||
| path_index: ~ | ||
| step: samplesheet | ||
| tag: samplesheet | ||
| - format: yaml | ||
| id: CASEID | ||
| path: PATHTOCASE/CASEID_params_file.yaml | ||
| path_index: ~ | ||
| step: nextflow-params | ||
| tag: nextflow-params | ||
| - format: json | ||
| id: CASEID | ||
| path: PATHTOCASE/CASEID_nextflow_config.json | ||
| path_index: ~ | ||
| step: nextflow-config | ||
| tag: nextflow-config | ||
| - format: json | ||
| id: CASEID | ||
| path: PATHTOCASE/manifest.json | ||
| path_index: ~ | ||
| step: manifest | ||
| tag: manifest |