digraph workflow {
	graph [_draw_="c 9 -#fffffe00 C 7 -#eeeeee P 4 0 0 0 233 1005.5 233 1005.5 0 ",
		bb="0,0,1005.5,233",
		bgcolor="#eeeeee",
		clusterrank=local,
		color=black,
		dpi=96,
		fontsize=10,
		labeljust=left,
		nodesep=0.05,
		ranksep=0.22,
		xdotversion=1.7
	];
	node [color=black,
		fillcolor=lightgoldenrodyellow,
		fontcolor=black,
		fontname=Helvetica,
		fontsize=10,
		height=0,
		label="\N",
		shape=record,
		style=filled,
		width=0
	];
	edge [arrowsize=0.7,
		color=black,
		fontcolor=black,
		fontname=Helvetica,
		fontsize=8
	];
	subgraph cluster_inputs {
		graph [_draw_="S 6 -dashed c 7 -#000000 C 7 -#eeeeee P 4 164 170 164 225 522 225 522 170 ",
			_ldraw_="F 10 11 -Times-Roman c 7 -#000000 T 214 213 0 84 15 -Workflow Inputs ",
			bb="164,170,522,225",
			label="Workflow Inputs",
			lheight=0.15,
			lp="214,215.5",
			lwidth=1.17,
			rank=same,
			style=dashed
		];
		threads	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 172 178.5 172 197.5 336 197.5 336 178.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 254 185.5 0 148 28 -Number of threads for Salmon ",
			fillcolor="#94DDF4",
			height=0.27778,
			label="Number of threads for Salmon",
			pos="254,188",
			rects="172,178.5,336,197.5",
			width=2.2778];
		fastq_dir	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 340.5 178.5 340.5 197.5 513.5 197.5 513.5 178.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 427 185.5 0 157 32 -Directory containing FASTQ files ",
			fillcolor="#94DDF4",
			height=0.27778,
			label="Directory containing FASTQ files",
			pos="427,188",
			rects="340.5,178.5,513.5,197.5",
			width=2.4028];
	}
	subgraph cluster_outputs {
		graph [_draw_="S 6 -dashed c 7 -#000000 C 7 -#eeeeee P 4 8 8 8 63 942 63 942 8 ",
			_ldraw_="F 10 11 -Times-Roman c 7 -#000000 T 62 15 0 92 16 -Workflow Outputs ",
			bb="8,8,942,63",
			label="Workflow Outputs",
			labelloc=b,
			lheight=0.15,
			lp="62,17.5",
			lwidth=1.28,
			rank=same,
			style=dashed
		];
		salmon_output	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 361.5 35.5 361.5 54.5 522.5 54.5 522.5 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 442 42.5 0 145 29 -Full output of `salmon quant` ",
			fillcolor="#94DDF4",
			height=0.27778,
			label="Full output of `salmon quant`",
			pos="442,45",
			rects="361.5,35.5,522.5,54.5",
			width=2.2361];
		expression_matrix	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 526.5 35.5 526.5 54.5 933.5 54.5 933.5 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 730 42.5 0 391 78 -A hd5 file containing transcript by sample matrices of TPM and number of reads ",
			fillcolor="#94DDF4",
			height=0.27778,
			label="A hd5 file containing transcript by sample matrices of TPM and number of reads",
			pos="730,45",
			rects="526.5,35.5,933.5,54.5",
			width=5.6528];
		fastqc_dir	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 16.5 35.5 16.5 54.5 357.5 54.5 357.5 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 187 42.5 0 325 69 -Directory of FastQC output files, mirroring input directory structure ",
			fillcolor="#94DDF4",
			height=0.27778,
			label="Directory of FastQC output files, mirroring input directory structure",
			pos="187,45",
			rects="16.5,35.5,357.5,54.5",
			width=4.7361];
	}
	fastqc	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 86 125.5 86 144.5 336 144.5 336 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 211 132.5 0 234 49 -Runs fastQC on each fastq file in fastq directory ",
		height=0.27778,
		label="Runs fastQC on each fastq file in fastq directory",
		pos="211,135",
		rects="86,125.5,336,144.5",
		width=3.4722];
	threads -> fastqc	[_draw_="c 7 -#000000 B 4 246.9 178.58 240.51 171 230.99 159.71 223.35 150.65 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 225.33 149.19 218.94 145.42 221.58 152.35 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 248 155.6 0 32 7 -threads ",
		label=threads,
		lp="248,157.5",
		pos="e,217.97,144.26 246.9,178.58 240.51,171 230.99,159.71 223.35,150.65"];
	"salmon-bulk"	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 340 125.5 340 144.5 544 144.5 544 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 442 132.5 0 188 36 -Run Salmon quant tool on FASTQ input ",
		height=0.27778,
		label="Run Salmon quant tool on FASTQ input",
		pos="442,135",
		rects="340,125.5,544,144.5",
		width=2.8333];
	threads -> "salmon-bulk"	[_draw_="c 7 -#000000 B 7 272.29 178.57 289.64 170.89 316.62 159.74 341 153 350.67 150.33 360.98 148.01 371.19 146.01 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 371.41 148.46 377.84 144.76 370.51 143.65 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 357 155.6 0 32 7 -threads ",
		label=threads,
		lp="357,157.5",
		pos="e,379.33,144.48 272.29,178.57 289.64,170.89 316.62,159.74 341,153 350.67,150.33 360.98,148.01 371.19,146.01"];
	fastq_dir -> fastqc	[_draw_="c 7 -#000000 B 7 416.34 178.7 405.38 170.66 387.49 158.84 370 153 361.46 150.15 347.03 147.65 330.25 145.51 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 330.59 143.08 323.35 144.67 330 147.95 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 407 155.6 0 36 9 -fastq_dir ",
		label=fastq_dir,
		lp="407,157.5",
		pos="e,321.84,144.49 416.34,178.7 405.38,170.66 387.49,158.84 370,153 361.46,150.15 347.03,147.65 330.25,145.51"];
	fastq_dir -> "salmon-bulk"	[_draw_="c 7 -#000000 B 4 429.48 178.58 431.57 171.45 434.64 161.02 437.21 152.27 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 439.52 153.12 439.14 145.72 434.82 151.74 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 454 155.6 0 36 9 -fastq_dir ",
		label=fastq_dir,
		lp="454,157.5",
		pos="e,439.57,144.26 429.48,178.58 431.57,171.45 434.64,161.02 437.21,152.27"];
	fastqc -> fastqc_dir	[_draw_="c 7 -#000000 B 4 208.7 125.56 204.75 111.07 196.6 81.21 191.49 62.47 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 193.86 61.85 189.66 55.74 189.14 63.14 ",
		pos="e,189.26,54.284 208.7,125.56 204.75,111.07 196.6,81.205 191.49,62.471"];
	"salmon-bulk" -> salmon_output	[_draw_="c 7 -#000000 B 4 442 125.56 442 111.14 442 81.48 442 62.73 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 444.45 62.8 442 55.8 439.55 62.8 ",
		pos="e,442,54.284 442,125.56 442,111.14 442,81.476 442,62.727"];
	make_expression_matrix	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 450.5 80.5 450.5 99.5 1005.5 99.5 1005.5 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 728 87.5 0 539 103 -Takes gene expression vectors from several bulk RNA samples and makes them \
into a gene by sample matrix ",
		height=0.27778,
		label="Takes gene expression vectors from several bulk RNA samples and makes them into a gene by sample matrix",
		pos="728,90",
		rects="450.5,80.5,1005.5,99.5",
		width=7.7083];
	"salmon-bulk" -> make_expression_matrix	[_draw_="c 7 -#000000 B 4 498.5 125.5 545.9 118.38 613.61 108.2 663.2 100.74 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 663.56 103.17 670.12 99.7 662.83 98.32 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 629.5 110.6 0 39 9 -quant_dir ",
		label=quant_dir,
		lp="629.5,112.5",
		pos="e,671.61,99.478 498.5,125.5 545.9,118.38 613.61,108.2 663.2,100.74"];
	make_expression_matrix -> expression_matrix	[_draw_="c 7 -#000000 B 4 728.39 80.71 728.62 75.59 728.94 68.85 729.22 62.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 731.67 62.88 729.55 55.78 726.77 62.66 ",
		pos="e,729.62,54.265 728.39,80.709 728.62,75.593 728.94,68.848 729.22,62.666"];
}
