digraph workflow {
	graph [_draw_="c 9 -#fffffe00 C 7 -#eeeeee P 4 0 0 0 233 1004.5 233 1004.5 0 ",
		bb="0,0,1004.5,233",
		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 4 252 170 252 225 676 225 676 170 ",
			_ldraw_="F 10 11 -Times-Roman c 7 -#000000 T 302 213 0 84 15 -Workflow Inputs ",
			bb="252,170,676,225",
			label="Workflow Inputs",
			lheight=0.15,
			lp="302,215.5",
			lwidth=1.17,
			rank=same,
			style=dashed
		];
		threads	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 438 178.5 438 197.5 602 197.5 602 178.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 520 185.5 0 148 28 -Number of threads for Salmon ",
			fillcolor="#94DDF4",
			height=0.27778,
			label="Number of threads for Salmon",
			pos="520,188",
			rects="438,178.5,602,197.5",
			width=2.2778];
		fastq_dir	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 260.5 178.5 260.5 197.5 433.5 197.5 433.5 178.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 347 185.5 0 157 32 -Directory containing FASTQ files ",
			fillcolor="#94DDF4",
			height=0.27778,
			label="Directory containing FASTQ files",
			pos="347,188",
			rects="260.5,178.5,433.5,197.5",
			width=2.4028];
		organism	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 606 178.5 606 197.5 668 197.5 668 178.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 637 185.5 0 46 8 -organism ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=organism,
			pos="637,188",
			rects="606,178.5,668,197.5",
			width=0.86111];
	}
	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
		];
		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];
		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];
		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];
	}
	"salmon-bulk"	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 378 125.5 378 144.5 582 144.5 582 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 480 132.5 0 188 36 -Run Salmon quant tool on FASTQ input ",
		height=0.27778,
		label="Run Salmon quant tool on FASTQ input",
		pos="480,135",
		rects="378,125.5,582,144.5",
		width=2.8333];
	threads -> "salmon-bulk"	[_draw_="c 7 -#000000 B 4 513.39 178.58 507.51 171.08 498.77 159.93 491.7 150.92 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 493.66 149.45 487.42 145.46 489.81 152.48 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 516 155.6 0 32 7 -threads ",
		label=threads,
		lp="516,157.5",
		pos="e,486.48,144.26 513.39,178.58 507.51,171.08 498.77,159.93 491.7,150.92"];
	"salmon-bulk-mouse"	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 586 125.5 586 144.5 790 144.5 790 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 688 132.5 0 188 36 -Run Salmon quant tool on FASTQ input ",
		height=0.27778,
		label="Run Salmon quant tool on FASTQ input",
		pos="688,135",
		rects="586,125.5,790,144.5",
		width=2.8333];
	threads -> "salmon-bulk-mouse"	[_draw_="c 7 -#000000 B 10 564.24 178.53 593.55 172.72 627.71 165.44 634 162 638.96 159.28 638.25 156.07 643 153 645.92 151.11 649.08 149.39 \
652.33 147.83 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 653.16 150.14 658.59 145.08 651.2 145.65 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 659 155.6 0 32 7 -threads ",
		label=threads,
		lp="659,157.5",
		pos="e,659.98,144.48 564.24,178.53 593.55,172.72 627.71,165.44 634,162 638.96,159.28 638.25,156.07 643,153 645.92,151.11 649.08,149.39 \
652.33,147.83"];
	fastqc	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 124 125.5 124 144.5 374 144.5 374 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 249 132.5 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="249,135",
		rects="124,125.5,374,144.5",
		width=3.4722];
	threads -> fastqc	[_draw_="c 7 -#000000 B 7 501.19 178.51 482.71 170.55 453.49 159 427 153 415.1 150.3 393.72 147.66 369.81 145.29 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 370.33 142.88 363.12 144.64 369.85 147.76 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 474 155.6 0 32 7 -threads ",
		label=threads,
		lp="474,157.5",
		pos="e,361.62,144.5 501.19,178.51 482.71,170.55 453.49,159 427,153 415.1,150.3 393.72,147.66 369.81,145.29"];
	fastq_dir -> "salmon-bulk"	[_draw_="c 7 -#000000 B 7 355.98 178.66 364.93 170.82 379.41 159.35 394 153 399.69 150.52 405.75 148.4 411.92 146.59 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 412.2 149.05 418.31 144.85 410.91 144.32 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 412 155.6 0 36 9 -fastq_dir ",
		label=fastq_dir,
		lp="412,157.5",
		pos="e,419.77,144.45 355.98,178.66 364.93,170.82 379.41,159.35 394,153 399.69,150.52 405.75,148.4 411.92,146.59"];
	fastq_dir -> "salmon-bulk-mouse"	[_draw_="c 7 -#000000 B 13 387.63 178.53 403.32 175.49 421.44 172.26 438 170 458.33 167.22 511.66 171.21 530 162 534.78 159.6 533.25 155.46 \
538 153 542.8 150.51 560.07 147.86 581.28 145.41 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 581.39 147.87 588.08 144.66 580.85 143 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 556 155.6 0 36 9 -fastq_dir ",
		label=fastq_dir,
		lp="556,157.5",
		pos="e,589.58,144.49 387.63,178.53 403.32,175.49 421.44,172.26 438,170 458.33,167.22 511.66,171.21 530,162 534.78,159.6 533.25,155.46 \
538,153 542.8,150.51 560.07,147.86 581.28,145.41"];
	fastq_dir -> fastqc	[_draw_="c 7 -#000000 B 4 330.82 178.58 314.93 170.31 290.52 157.61 272.5 148.23 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 273.89 146.19 266.55 145.13 271.63 150.54 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 316 155.6 0 36 9 -fastq_dir ",
		label=fastq_dir,
		lp="316,157.5",
		pos="e,265.21,144.43 330.82,178.58 314.93,170.31 290.52,157.61 272.5,148.23"];
	organism -> "salmon-bulk"	[_draw_="c 7 -#000000 B 7 624.74 178.71 612.62 170.89 593.29 159.46 575 153 567.59 150.39 559.71 148.16 551.78 146.27 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 552.7 143.96 545.33 144.81 551.62 148.74 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 613.5 155.6 0 39 8 -organism ",
		label=organism,
		lp="613.5,157.5",
		pos="e,543.85,144.48 624.74,178.71 612.62,170.89 593.29,159.46 575,153 567.59,150.39 559.71,148.16 551.78,146.27"];
	organism -> "salmon-bulk-mouse"	[_draw_="c 7 -#000000 B 7 654.52 178.62 661.88 174.43 670.08 168.79 676 162 678.5 159.13 680.57 155.66 682.26 152.19 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 684.48 153.22 684.91 145.82 679.96 151.34 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 700.5 155.6 0 39 8 -organism ",
		label=organism,
		lp="700.5,157.5",
		pos="e,685.49,144.42 654.52,178.62 661.88,174.43 670.08,168.79 676,162 678.5,159.13 680.57,155.66 682.26,152.19"];
	"salmon-bulk" -> salmon_output	[_draw_="c 7 -#000000 B 7 469.57 125.63 462.53 119.36 453.7 110.15 449 100 443.6 88.34 441.96 73.84 441.61 62.8 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 444.06 62.98 441.57 55.99 439.16 63 ",
		pos="e,441.57,54.478 469.57,125.63 462.53,119.36 453.7,110.15 449,100 443.6,88.341 441.96,73.838 441.61,62.798"];
	make_expression_matrix	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 449.5 80.5 449.5 99.5 1004.5 99.5 1004.5 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 727 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="727,90",
		rects="449.5,80.5,1004.5,99.5",
		width=7.7083];
	"salmon-bulk" -> make_expression_matrix	[_draw_="c 7 -#000000 B 4 528.8 125.5 569.4 118.44 627.24 108.37 669.97 100.93 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 670.33 103.35 676.81 99.74 669.49 98.52 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 644.5 110.6 0 39 9 -quant_dir ",
		label=quant_dir,
		lp="644.5,112.5",
		pos="e,678.3,99.478 528.8,125.5 569.4,118.44 627.24,108.37 669.97,100.93"];
	"salmon-bulk-mouse" -> make_expression_matrix	[_draw_="c 7 -#000000 B 4 695.52 125.71 700.7 120 707.72 112.26 713.82 105.54 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 715.6 107.22 718.49 100.39 711.97 103.93 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 729.5 110.6 0 39 9 -quant_dir ",
		label=quant_dir,
		lp="729.5,112.5",
		pos="e,719.5,99.265 695.52,125.71 700.7,120 707.72,112.26 713.82,105.54"];
	make_expression_matrix -> expression_matrix	[_draw_="c 7 -#000000 B 4 727.58 80.71 727.94 75.59 728.41 68.85 728.84 62.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 731.27 62.93 729.32 55.78 726.39 62.59 ",
		pos="e,729.42,54.265 727.58,80.709 727.94,75.593 728.41,68.848 728.84,62.666"];
	fastqc -> fastqc_dir	[_draw_="c 7 -#000000 B 4 243.06 125.56 232.57 110.67 210.65 79.56 197.54 60.96 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 199.74 59.83 193.71 55.52 195.74 62.65 ",
		pos="e,192.84,54.284 243.06,125.56 232.57,110.67 210.65,79.565 197.54,60.963"];
}