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rjchallisrjchallis
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add mermaid pipelne diagram
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‎README.md

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@@ -85,6 +85,68 @@ docker run -it --rm --name blobtools -p 8000:8000 -p 8001:8001 genomehubs/blobto
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## BlobToolKit pipeline
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```mermaid
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%%{ init: { 'flowchart': { 'curve': 'step' } } }%%
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flowchart TD
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Assembly:::inputclass@{ shape: document, label: "Assembly *FASTA*"} --> windowmasker:::processclass
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windowmasker --> MaskedAssembly:::fileclass@{ shape: document, label: "Masked assembly *FASTA*"}
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MaskedAssembly --> BUSCO:::processclass
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BUSCO --> BuscoFullTable:::fileclass@{ shape: documents, label: "BUSCO full table *TSV*"}
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MaskedAssembly --> chunk_fasta:::processclass
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BuscoFullTable --> chunk_fasta
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NT:::inputclass@{ shape: database, label: "NCBI\nnt"} -.-> blastn:::processclass
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chunk_fasta --> BuscoRegions:::fileclass@{ shape: documents, label: "BUSCO regions *FASTA*"}
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BUSCO --> BuscoSequences:::fileclass@{ shape: documents, label: "BUSCO sequences *FASTA*"}
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BuscoSequences --> extract_busco_genes:::processclass
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extract_busco_genes --> BuscoGenes:::fileclass@{ shape: documents, label: "BUSCO genes *FASTA*"}
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Uniprot:::inputclass@{ shape: database, label: "UniProt\nUniRef 90"} --> blastx[diamond blastx]:::processclass
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MaskedAssembly --> minimap2:::processclass
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Reads:::inputclass@{ shape: documents, label: "Read *FASTQ*"} --> minimap2
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minimap2 --> CRAM:::fileclass@{ shape: documents, label: "mapped reads *BAM*/*CRAM*"}
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BuscoRegions --> blastx
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BuscoGenes --> blastp[diamond blastp]:::processclass
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Uniprot --> blastp
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blastx --> blastxOut:::fileclass@{ shape: document, label: "blastx results *TSV*"}
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blastp --> blastpOut:::fileclass@{ shape: document, label: "blastp results *TSV*"}
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blastxOut --> filter_chunks:::processclass
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BuscoRegions --> filter_chunks
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filter_chunks -.-> filteredChunks:::fileclass@{ shape: document, label: "no-hit regions *FASTA*"}
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blastn -.-> blastnOut:::fileclass@{ shape: document, label: "blastn results *TSV*"}
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filteredChunks -.-> blastn
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CRAM --> blobtk_depth[blobtk depth]:::processclass
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blobtk_depth --> readDepth:::fileclass@{ shape: documents, label: "read coverage depth *BED*"}
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BuscoFullTable --> count_busco_genes:::processclass
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MaskedAssembly --> fasta_windows:::processclass
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count_busco_genes --> BuscoGeneCounts:::fileclass@{ shape: document, label: "BUSCO gene counts *BED*"}
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fasta_windows --> KmerStats:::fileclass@{ shape: documents, label: "kmer stats *BED*"}
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BuscoGeneCounts --> combine_outputs:::processclass
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KmerStats --> combine_outputs
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NCBITaxonomy:::inputclass@{ shape: database, label: "NCBI taxonomy"} --> blobtools_create[blobtools create]:::processclass
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blastpOut --> blobtools_create
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blastxOut --> blobtools_add
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blastnOut --> blobtools_add
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readDepth --> combine_outputs
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combine_outputs --> kbStats:::fileclass@{ shape: document, label: "1kb assembly stats *BED*"}
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kbStats --> window_stats:::processclass
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window_stats --> windowStats:::fileclass@{ shape: documents, label: "100kb, 1Mb, 1% & 10% window stats *BED*"}
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windowStats --> blobtools_create
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blobtools_create --> BlobDir:::fileclass@{ shape: documents, label: "Initial *BlobDir*"}
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NCBITaxonomy --> blobtools_add
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BlobDir --> blobtools_add[blobtools add]:::processclass
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BlobDir --> blobtools_filter[blobtools filter --summary]:::processclass
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BlobDir --> blobtk_plot[blobtk plot]:::processclass
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blobtools_add --> FullBlobDir:::fileclass@{ shape: documents, label: "Complete *BlobDir*"}
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blobtools_filter --> FullBlobDir
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blobtk_plot --> FullBlobDir
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classDef inputclass fill:#f969,stroke-width:4px
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classDef processclass fill:#96f9,stroke-width:4px
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classDef fileclass fill:#6f99,stroke-width:4px
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classDef default stroke-width:4px;
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linkStyle default stroke-width:4px;
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```
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The BlobToolKit pipeline can be run by creating a YAML config file and environment variables to the `genomehubs/blobtoolkit` docker image.
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```sh

‎pipeline.mermaid

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flowchart TD
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Assembly@{ shape: document, label: "Assembly *FASTA*"} --> windowmasker
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windowmasker --> MaskedAssembly@{ shape: document, label: "Masked assembly *FASTA*"}
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MaskedAssembly --> fasta_windows
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MaskedAssembly --> BUSCO
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BUSCO --> BuscoFullTable@{ shape: documents, label: "BUSCO full table *TSV*"}
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BuscoFullTable --> chunk_fasta
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MaskedAssembly --> chunk_fasta
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NT@{ shape: database, label: "NCBI\nnt"} -.-> blastn
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chunk_fasta --> BuscoRegions@{ shape: documents, label: "BUSCO regions *FASTA*"}
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BUSCO --> BuscoSequences@{ shape: documents, label: "BUSCO sequences *FASTA*"}
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BuscoSequences --> extract_busco_genes
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extract_busco_genes --> BuscoGenes@{ shape: documents, label: "BUSCO genes *FASTA*"}
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Uniprot@{ shape: database, label: "UniProt\nUniRef 90"} --> blastx[diamond blastx]
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MaskedAssembly --> minimap2
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Reads@{ shape: documents, label: "Read *FASTQ*"} --> minimap2
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fasta_windows --> KmerStats@{ shape: documents, label: "kmer stats *BED*"}
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minimap2 --> CRAM@{ shape: documents, label: "mapped reads *BAM*/*CRAM*"}
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BuscoRegions --> blastx
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BuscoGenes --> blastp
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Uniprot --> blastp[diamond blastp]
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blastx --> blastxOut@{ shape: document, label: "blastx results *TSV*"}
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blastp --> blastpOut@{ shape: document, label: "blastp results *TSV*"}
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blastxOut --> filter_chunks
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BuscoRegions --> filter_chunks
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filter_chunks -.-> filteredChunks@{ shape: document, label: "no-hit regions *FASTA*"}
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blastn -.-> blastnOut@{ shape: document, label: "blastn results *TSV*"}
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filteredChunks -.-> blastn
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CRAM --> blobtk_depth[blobtk depth]
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blobtk_depth --> readDepth@{ shape: documents, label: "read coverage depth *BED*"}
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BuscoFullTable --> count_busco_genes
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count_busco_genes --> BuscoGeneCounts@{ shape: document, label: "BUSCO gene counts *BED*"}
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KmerStats --> combine_outputs
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NCBITaxonomy@{ shape: database, label: "NCBI taxonomy"} --> blobtools_create[blobtools create]
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blastpOut --> blobtools_create
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BuscoGeneCounts --> combine_outputs
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blastxOut --> blobtools_add
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blastnOut --> blobtools_add
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readDepth --> combine_outputs
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combine_outputs --> kbStats@{ shape: document, label: "1kb assembly stats *BED*"}
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kbStats --> window_stats
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window_stats --> windowStats@{ shape: documents, label: "100kb, 1Mb, 1% & 10% window stats *BED*"}
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windowStats --> blobtools_create
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blobtools_create --> BlobDir@{ shape: documents, label: "Initial *BlobDir*"}
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NCBITaxonomy@{ shape: database, label: "NCBI taxonomy"} --> blobtools_add
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BlobDir --> blobtools_add[blobtools add]
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BlobDir --> blobtools_filter[blobtools_filter --summary]
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BlobDir --> blobtk_plot[blobtk plot]
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blobtools_add --> FullBlobDir@{ shape: documents, label: "Complete *BlobDir*"}
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blobtools_filter --> FullBlobDir
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blobtk_plot --> FullBlobDir

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