Workflow¶
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flowchart TB
subgraph "Subworkflow: vcf"
subgraph "annotate"
va0[AnnotSV]
va1[Stranger]
va2{SpliceAI?}
va3[CAPICE]
va4[VEP]
va4t[(per project:
project_annotations.vcf.gz)] va0-->va1 va1-->va2 va2-->|"true"|va3 va2-->|"false"|va4 va3-->va4 va4-->va4t end v0{Phenotypes?} v1[GADO] v2[Normalize] v3[Classify] v3t[(per project:
project_classifications.vcf.gz)] v4[Filter] v5[Inheritance] v6[Classify samples] v6t[(per project:
project_sample_classifications.vcf.gz)] v7[Filter samples] v8{Cram?} v9[Slice] v10[Report] v10t0[(per project:
project.html)] v10t1[(per project:
project.vcf.gz)] v10t2[(per project:
project.db)] v0-->|"true"|v1 v0-->|"false"|v2 v1-->v2 v2-->va0 v3-->v3t v3-->v4 v4-->v5 v5-->v6 v6-->v6t v6-->v7 v7-->v8 v8-->|"true"|v9 v8-->|"false"|v10 v9-->v10 v10-->v10t0 v10-->v10t1 v10-->v10t2 va4-->v3 end subgraph "Workflow: vcf" wv([Start]) wv0[Validate VCF] wv1{Regions?} wv2[Filter] wv3{Liftover?} wv4[Liftover] wv4t[(per project:
project_liftover_accepted.vcf.gz
project_liftover_rejected.vcf.gz)] wv5{Cram?} wv6[Validate Cram] wv7@{ shape: f-circ, label: "Junction" } wv-->wv0 wv0-->wv1 wv1-->|"true"|wv2 wv1-->|"false"|wv3 wv2-->wv3 wv3-->|"true"|wv4 wv3-->|"false"|wv5 wv4-->wv4t wv4-->wv7 wv5-->wv6 wv5-->|"true"|wv7 wv6-->|"false"|wv7 wv7-->v0 end subgraph "Subworkflow: gvcf" g0[GLnexus] g0t[(per sample chunk:
sample_chunk.vcf.gz)] g0-->g0t g0-->v0 end subgraph "Workflow: gvcf" wg([Start]) wg0[Validate gVCF] wg1{Regions?} wg2[Filter] wg3{Liftover?} wg4[Liftover] wg4t[(per sample:
sample_liftover_accepted.vcf.gz
sample_liftover_rejected.vcf.gz)] wg5{Cram?} wg6[Validate Cram] wg7@{ shape: f-circ, label: "Junction" } wg-->wg0 wg0-->wg1 wg1-->|"true"|wg2 wg1-->|"false"|wg3 wg2-->wg3 wg3-->|"true"|wg4 wg3-->|"false"|wg5 wg4-->wg4t wg4-->wg7 wg5-->wg6 wg5-->wg7 wg6-->wg7 wg7-->g0 end subgraph "Subworkflow: cram" subgraph "Subworkflow: cnv" cc0{Sequencing platform?} cc1[Spectre] cc1t[(per sample:
sample_cnv.vcf.gz)] cc2@{ shape: f-circ, label: "Junction" } cc0-->|"nanopore
pacbio_hifi"|cc1 cc0-->|"illumina"|cc2 cc1-->cc1t cc1-->cc2 cc0-->cc2 end subgraph "Subworkflow: snv" cn0{Sequencing platform?} cn1{Trio or duo?} cn2[Deeptrio] cn3[Deepvariant] cn4[GLnexus] cn5[WhatsHap] cn6[Concat VCF] cn6t[(per project:
project_snv.vcf.gz)] cn7@{ shape: f-circ, label: "Junction" } cn0-->|"illumina
pacbio_hifi"|cn1 cn0-->|"nanopore"|cn3 cn1-->|"true"|cn2 cn1-->|"false"|cn3 cn2-->cn4 cn3-->cn4 cn4-->cn5 cn5-->cn6 cn6-->cn6t cn6-->cn7 end subgraph "Subworkflow: str" ct0{PCR performed?} ct1{Sequencing platform?} ct2[Expansion Hunter] ct3[Straglr] ct2-3t[(per sample:
sample_str.vcf.gz)] ct4@{ shape: f-circ, label: "Junction" } ct0-->|"false"|ct1 ct0-->|"true"|ct4 ct1-->|"illumina"|ct2 ct1-->|"nanopore
pacbio_hifi"|ct3 ct2-->ct2-3t ct2-->ct4 ct3-->ct2-3t ct3-->ct4 end subgraph "Subworkflow: sv" cv0{Sequencing platform?} cv1[Manta] cv1t[(per project:
project_sv.vcf.gz)] cv2[cuteSV] cv2t[(per sample:
sample_sv.vcf.gz)] cv3@{ shape: f-circ, label: "Junction" } cv0-->|"illumina"|cv1 cv0-->|"nanopore
pacbio_hifi"|cv2 cv1-->cv1t cv1-->cv3 cv2-->cv3 cv2-->cv2t end c0@{ shape: f-circ, label: "Junction" } c1[mosdepth] c1t[(per sample:
sample_mosdepth.global.dist.txt
sample_mosdepth.per-base.bed.gz
sample_mosdepth.region.dist.txt
sample_mosdepth.regions.bed.gz
sample_mosdepth.summary.txt
sample_mosdepth.thresholds.bed.gz)] c6[concat VCF] c6t[(per project
project.vcf.gz)] c7{Regions?} c8[Filter] c9@{ shape: f-circ, label: "Junction" } c0-->c1 c0-->cn0 c0-->ct0 c0-->cv0 c0-->cc0 c1-->c1t cn7-->c6 ct4-->c6 cv3-->c6 cc2-->c6 c6-->c6t c6-->c7 c7-->|"true"|c8 c7-->|"false"|c9 c8-->c9 c9-->v0 end subgraph "Workflow: cram" wc([Start]) wc0[Validate Cram] wc-->wc0 wc0-->c0 end subgraph "Subworkflow: fastq" f0{Adaptive sampling?} f1[Filter reads] f2[fastp] f2t[(per sample:
sample_pass.fastq.gz
sample_fail.fastq.gz
sample_report.html
sample_report.json)] f3[minimap2] f3t0[(per sample:
sample.cram)] f0-->|"true"|f1 f0-->|"false"|f2 f1-->f2 f2-->f2t f2-->f3 f3-->f3t0 f3-->c0 end subgraph "Workflow: fastq" wf([Start]) wf-->f0 end
project_annotations.vcf.gz)] va0-->va1 va1-->va2 va2-->|"true"|va3 va2-->|"false"|va4 va3-->va4 va4-->va4t end v0{Phenotypes?} v1[GADO] v2[Normalize] v3[Classify] v3t[(per project:
project_classifications.vcf.gz)] v4[Filter] v5[Inheritance] v6[Classify samples] v6t[(per project:
project_sample_classifications.vcf.gz)] v7[Filter samples] v8{Cram?} v9[Slice] v10[Report] v10t0[(per project:
project.html)] v10t1[(per project:
project.vcf.gz)] v10t2[(per project:
project.db)] v0-->|"true"|v1 v0-->|"false"|v2 v1-->v2 v2-->va0 v3-->v3t v3-->v4 v4-->v5 v5-->v6 v6-->v6t v6-->v7 v7-->v8 v8-->|"true"|v9 v8-->|"false"|v10 v9-->v10 v10-->v10t0 v10-->v10t1 v10-->v10t2 va4-->v3 end subgraph "Workflow: vcf" wv([Start]) wv0[Validate VCF] wv1{Regions?} wv2[Filter] wv3{Liftover?} wv4[Liftover] wv4t[(per project:
project_liftover_accepted.vcf.gz
project_liftover_rejected.vcf.gz)] wv5{Cram?} wv6[Validate Cram] wv7@{ shape: f-circ, label: "Junction" } wv-->wv0 wv0-->wv1 wv1-->|"true"|wv2 wv1-->|"false"|wv3 wv2-->wv3 wv3-->|"true"|wv4 wv3-->|"false"|wv5 wv4-->wv4t wv4-->wv7 wv5-->wv6 wv5-->|"true"|wv7 wv6-->|"false"|wv7 wv7-->v0 end subgraph "Subworkflow: gvcf" g0[GLnexus] g0t[(per sample chunk:
sample_chunk.vcf.gz)] g0-->g0t g0-->v0 end subgraph "Workflow: gvcf" wg([Start]) wg0[Validate gVCF] wg1{Regions?} wg2[Filter] wg3{Liftover?} wg4[Liftover] wg4t[(per sample:
sample_liftover_accepted.vcf.gz
sample_liftover_rejected.vcf.gz)] wg5{Cram?} wg6[Validate Cram] wg7@{ shape: f-circ, label: "Junction" } wg-->wg0 wg0-->wg1 wg1-->|"true"|wg2 wg1-->|"false"|wg3 wg2-->wg3 wg3-->|"true"|wg4 wg3-->|"false"|wg5 wg4-->wg4t wg4-->wg7 wg5-->wg6 wg5-->wg7 wg6-->wg7 wg7-->g0 end subgraph "Subworkflow: cram" subgraph "Subworkflow: cnv" cc0{Sequencing platform?} cc1[Spectre] cc1t[(per sample:
sample_cnv.vcf.gz)] cc2@{ shape: f-circ, label: "Junction" } cc0-->|"nanopore
pacbio_hifi"|cc1 cc0-->|"illumina"|cc2 cc1-->cc1t cc1-->cc2 cc0-->cc2 end subgraph "Subworkflow: snv" cn0{Sequencing platform?} cn1{Trio or duo?} cn2[Deeptrio] cn3[Deepvariant] cn4[GLnexus] cn5[WhatsHap] cn6[Concat VCF] cn6t[(per project:
project_snv.vcf.gz)] cn7@{ shape: f-circ, label: "Junction" } cn0-->|"illumina
pacbio_hifi"|cn1 cn0-->|"nanopore"|cn3 cn1-->|"true"|cn2 cn1-->|"false"|cn3 cn2-->cn4 cn3-->cn4 cn4-->cn5 cn5-->cn6 cn6-->cn6t cn6-->cn7 end subgraph "Subworkflow: str" ct0{PCR performed?} ct1{Sequencing platform?} ct2[Expansion Hunter] ct3[Straglr] ct2-3t[(per sample:
sample_str.vcf.gz)] ct4@{ shape: f-circ, label: "Junction" } ct0-->|"false"|ct1 ct0-->|"true"|ct4 ct1-->|"illumina"|ct2 ct1-->|"nanopore
pacbio_hifi"|ct3 ct2-->ct2-3t ct2-->ct4 ct3-->ct2-3t ct3-->ct4 end subgraph "Subworkflow: sv" cv0{Sequencing platform?} cv1[Manta] cv1t[(per project:
project_sv.vcf.gz)] cv2[cuteSV] cv2t[(per sample:
sample_sv.vcf.gz)] cv3@{ shape: f-circ, label: "Junction" } cv0-->|"illumina"|cv1 cv0-->|"nanopore
pacbio_hifi"|cv2 cv1-->cv1t cv1-->cv3 cv2-->cv3 cv2-->cv2t end c0@{ shape: f-circ, label: "Junction" } c1[mosdepth] c1t[(per sample:
sample_mosdepth.global.dist.txt
sample_mosdepth.per-base.bed.gz
sample_mosdepth.region.dist.txt
sample_mosdepth.regions.bed.gz
sample_mosdepth.summary.txt
sample_mosdepth.thresholds.bed.gz)] c6[concat VCF] c6t[(per project
project.vcf.gz)] c7{Regions?} c8[Filter] c9@{ shape: f-circ, label: "Junction" } c0-->c1 c0-->cn0 c0-->ct0 c0-->cv0 c0-->cc0 c1-->c1t cn7-->c6 ct4-->c6 cv3-->c6 cc2-->c6 c6-->c6t c6-->c7 c7-->|"true"|c8 c7-->|"false"|c9 c8-->c9 c9-->v0 end subgraph "Workflow: cram" wc([Start]) wc0[Validate Cram] wc-->wc0 wc0-->c0 end subgraph "Subworkflow: fastq" f0{Adaptive sampling?} f1[Filter reads] f2[fastp] f2t[(per sample:
sample_pass.fastq.gz
sample_fail.fastq.gz
sample_report.html
sample_report.json)] f3[minimap2] f3t0[(per sample:
sample.cram)] f0-->|"true"|f1 f0-->|"false"|f2 f1-->f2 f2-->f2t f2-->f3 f3-->f3t0 f3-->c0 end subgraph "Workflow: fastq" wf([Start]) wf-->f0 end