Complete Pipeline Flowchart

flowchart TD
subgraph Basecalling -- NanoMetaBasecall
	direction TB
	a[/Reads/] 
	a1[Guppy basecaller]
	a2{"High or Super accuracy model?"}
	a3[\Basecalled reads\]
	end
subgraph NanoMetaPipe
    subgraph Main Pipeline
	direction TB
		subgraph PreChecks
			b1[User options] 
			b2{Reads: \ndscDNA \nand/or \nDNA}
			b3{Transcriptome: \ncreate \nor provided}
			b8{Demultiplexer:\n Qcat or Guppy}
			b10[Choice]
			b5{Transcript \nreads and \nadapters?}
			b9[Ask user to \nprovide reads \nand adapters]
			b7([End])
		end
		subgraph Demultiplexing
			d1[Demultiplex \nbasecalled reads] 
			d2[(Zipped \ndemultiplexed \nreads)]
			d3[Filter for \nlength and \nquality]
			d4[Rename files]
			d5[(Filtered \ndemultiplexed \nreads)]
			d6[AssemblyStats \nand FastQC \noutputs]
		end
		subgraph Alignment
			al1{DNA or \ncDNA reads?}
			al2[Align vs DNA ref]
			al3[Align vs cDNA]
			al4[Flagstat BAM]
			al5[(Unaligned \nreads)]
		end
		subgraph Assembly
			As1[de novo \nmetagenomic \nassembly]
			As2[Metagenomes]
			As3[metaQuast outputs]
			As4[AssemblyStats outputs]
		end
		subgraph Kraken/Bracken
			kb1{cDNA or DNA}
			kb2{Assembly or Reads}
			kb3[Kraken taxonomic classification]
			kb4[Bracken re-estimation]
		end
    end
end
subgraph Functions
	subgraph Functions in Tools.py
	direction TB
		t1[makeDirectory: checks and \nmakes a folder]
		t2[zipFiles: zips files]
		t3[filter_fastq_file: remove \nduplicate \nnames before Flye]
		t4[run_flye: metaflye \nde-novo \nassembly]
		t5[run_AssemStats: carry out \nassembly-stats \non fasta/q]
		t6[raw_Quast: carry out \nquast assessment \nof metagenomes]
		t7[krakBrak: do kraken \nand bracken for reads \nand assembly]
	end
	subgraph Functions in Preprocessing.py
	direction TB
		p1[demultip: do \ndemultiplexing]
		p2[dna_filter: calls filt_qc \nto filter DNA \nand format output]
		p3[cdna_filter: calls filt_qc \nto filter DNA \nand format output]
		p4[filt_qc: do filtering \nusing Nanofilt]
		p5[run_QC: QCs reads \nwith NanoStat, \nNanoQC and FastQC]
	end
	subgraph Functions in DNA_processing.py
	direction 
		dp1[align: index \nand align \nreads vs ref]
		dp2[DNA_align: calls \nalign func. \nto align DNA reads]
		dp3[cDNA_align: make/align \ntransciptome vs \ncDNA reads]
	end	
end
	a --> a1
	a1 --> a2
	a2 --> a3
	b1 --> b2
	b2 --dscDNA--> b3
	b2 --DNA--> b8
	b3 --create--> b5
	b3 --provided--> b8
	b5 --No--> b9
	b5 --Yes--> b8
	b9 --> b7
	d1 --> d2
	d2 --> d3
	d3 --> d4
	d4 --> d5
	d2 -...-> d6
	d5 -...-> d6
	b10 --> d1
	a3 --> d1
	p1 -.-> d1
	t2 -.-> d2
	p5 -.-> d2
	p2 -.-> d3
	p3 -.-> d3
	p5 -.-> d5
	d5 --> al1
	t1 -..-> dp2
	t1 -..-> dp3
	t3 -..-> dp2
	t3 -..-> dp3
	al1 --DNA--> al2
	al1--cDNA-->al3
	al2-.->al4
	al2 --> al5
	al3 --> al5
	dp2 -..-> al2
	dp3 -..-> al3
	dp1 --> dp2
	t1 -..-> As1
	al5 --> As1
	t4 -..-> As1
	As1 --> As2
	t5 -...-> As2
	t6 -...-> As2
	As2 -..-> As3
	As2 -..-> As4
	As2 --> kb1
	kb1 --cDNA--> kb2
	kb1 --DNA--> kb2
	kb2 --Assembly--> kb3
	kb2 --Reads--> kb3
	kb3 --> kb4
	t7 -..-> kb3
	t7 -..-> kb4
	p4 --> p2
	p4 --> p3
	b8 --> b10
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