Commit 7ec7dba2 authored by Raphael Müller's avatar Raphael Müller
Browse files

Graph mermaid

parent d8bbc2fb
......@@ -96,15 +96,67 @@ Optional Options: [default]
## Graphical description
```mermaid
graph Backmap
Assembly --> BWAIndex[BWA Index]
Assembly --> Minimap[Minimap 2]
BWAIndex -- Index Files --> BWAMem[BWA Mem]
SER[Single-end Reads] --> BWAMem
PER[Paired-end Reads] --> BWAMem
end
graph TD;
Assembly --> BWAIndex{bwa index};
Assembly --> MinimapP{minimap2};
Assembly --> MinimapN{minimap2};
BWAI --> BWAMemSE{bwa mem};
BWAI --> BWAMemPE{bwa mem};
subgraph Illumina
BWAIndex{bwa index} --> BWAI[BWA Index Files];
SER[[Single-end Reads]] --> BWAMemSE;
PER[[Paired-end Reads]] --> BWAMemPE;
BWAMemSE --> SEBam[[Single-end Mapped Reads]] --> SMI{samtools merge};
BWAMemPE --> PEBam[[Paired-end Mapped Reads]] --> SMI{samtools merge};
SMI --> IMer[Illumina Merged Bam Files] --> SSI{samtools sort};
SSI --> ISor[Illumina Sorted Bam Files];
end
subgraph PacBio
PB[[PacBio Reads]] --> MinimapP;
MinimapP --> MBam[[Pacbio Mapped Reads]] --> SMP{samtools merge};
SMP --> PMer[Pacbio Merged Bam Files] --> SSP{samtools sort};
SSP --> PSor[Pacbio Sorted Bam Files];
end
subgraph Nanopore
ONT[[Nanopore Reads]] --> MinimapN;
MinimapN --> NBam[[Nanopore Mapped Reads]] --> SMN{samtools merge};
SMN --> NMer[Nanopore Merged Bam Files] --> SSN{samtools sort};
SSN --> NSor[Nanopore Sorted Bam Files];
end
subgraph Qualimap
ISor --> QMI{qualimap} --> MultiQC{{multiqc}}
PSor --> QMP{qualimap} --> MultiQC
NSor --> QMN{qualimap} --> MultiQC
end
subgraph RScripts
ISor --> bedI{bedtools genomecov} --> RCovSingleI{{"R Coverage Plot (single)"}}
PSor --> bedP{bedtools genomecov} --> RCovSingleP{{"R Coverage Plot (single)"}}
NSor --> bedN{bedtools genomecov} --> RCovSingleN{{"R Coverage Plot (single)"}}
bedI --> RCovMulti{{"R Coverage Plot (multi)"}}
bedP --> RCovMulti
bedN --> RCovMulti
end
subgraph Samtools Stat
ISor --> SSTI{{samtools stat}}
PSor --> SSTP{{samtools stat}}
NSor --> SSTN{{samtools stat}}
end
subgraph Genome Size Estimation
bedI --> GSEI{{Genome Size Estimation}}
bedP --> GSEP{{Genome Size Estimation}}
bedN --> GSEN{{Genome Size Estimation}}
Assembly --> GSEI
Assembly --> GSEP
Assembly --> GSEN
end
```
## Changes to the original perl pipeline
......
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