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 4 320.5 170 320.5 225 744.5 225 744.5 170 ",
			_ldraw_="F 10 11 -Times-Roman c 7 -#000000 T 370.5 213 0 84 15 -Workflow Inputs ",
			bb="320.5,170,744.5,225",
			label="Workflow Inputs",
			lheight=0.15,
			lp="370.5,215.5",
			lwidth=1.17,
			rank=same,
			style=dashed
		];
		threads	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 394.5 178.5 394.5 197.5 558.5 197.5 558.5 178.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 476.5 185.5 0 148 28 -Number of threads for Salmon ",
			fillcolor="#94DDF4",
			height=0.27778,
			label="Number of threads for Salmon",
			pos="476.5,188",
			rects="394.5,178.5,558.5,197.5",
			width=2.2778];
		fastq_dir	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 563 178.5 563 197.5 736 197.5 736 178.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 649.5 185.5 0 157 32 -Directory containing FASTQ files ",
			fillcolor="#94DDF4",
			height=0.27778,
			label="Directory containing FASTQ files",
			pos="649.5,188",
			rects="563,178.5,736,197.5",
			width=2.4028];
		organism	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 328.5 178.5 328.5 197.5 390.5 197.5 390.5 178.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 359.5 185.5 0 46 8 -organism ",
			fillcolor="#94DDF4",
			height=0.27778,
			label=organism,
			pos="359.5,188",
			rects="328.5,178.5,390.5,197.5",
			width=0.86111];
	}
	subgraph cluster_outputs {
		graph [_draw_="S 6 -dashed c 7 -#000000 C 7 -#eeeeee P 4 62.5 8 62.5 63 996.5 63 996.5 8 ",
			_ldraw_="F 10 11 -Times-Roman c 7 -#000000 T 116.5 15 0 92 16 -Workflow Outputs ",
			bb="62.5,8,996.5,63",
			label="Workflow Outputs",
			labelloc=b,
			lheight=0.15,
			lp="116.5,17.5",
			lwidth=1.28,
			rank=same,
			style=dashed
		];
		salmon_output	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 482 35.5 482 54.5 643 54.5 643 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 562.5 42.5 0 145 29 -Full output of `salmon quant` ",
			fillcolor="#94DDF4",
			height=0.27778,
			label="Full output of `salmon quant`",
			pos="562.5,45",
			rects="482,35.5,643,54.5",
			width=2.2361];
		fastqc_dir	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 647 35.5 647 54.5 988 54.5 988 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 817.5 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="817.5,45",
			rects="647,35.5,988,54.5",
			width=4.7361];
		expression_matrix	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 71 35.5 71 54.5 478 54.5 478 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 274.5 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="274.5,45",
			rects="71,35.5,478,54.5",
			width=5.6528];
	}
	"salmon-bulk-mouse"	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 197.5 125.5 197.5 144.5 401.5 144.5 401.5 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 299.5 132.5 0 188 36 -Run Salmon quant tool on FASTQ input ",
		height=0.27778,
		label="Run Salmon quant tool on FASTQ input",
		pos="299.5,135",
		rects="197.5,125.5,401.5,144.5",
		width=2.8333];
	threads -> "salmon-bulk-mouse"	[_draw_="c 7 -#000000 B 7 451.57 178.54 429.98 171.34 397.84 160.93 369.5 153 361.46 150.75 352.86 148.52 344.53 146.45 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 345.17 144.08 337.79 144.79 344 148.84 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 414.5 155.6 0 32 7 -threads ",
		label=threads,
		lp="414.5,157.5",
		pos="e,336.32,144.43 451.57,178.54 429.98,171.34 397.84,160.93 369.5,153 361.46,150.75 352.86,148.52 344.53,146.45"];
	"salmon-bulk"	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 405.5 125.5 405.5 144.5 609.5 144.5 609.5 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 507.5 132.5 0 188 36 -Run Salmon quant tool on FASTQ input ",
		height=0.27778,
		label="Run Salmon quant tool on FASTQ input",
		pos="507.5,135",
		rects="405.5,125.5,609.5,144.5",
		width=2.8333];
	threads -> "salmon-bulk"	[_draw_="c 7 -#000000 B 4 481.62 178.58 486.09 171.23 492.69 160.37 498.1 151.46 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 500.15 152.81 501.69 145.56 495.96 150.27 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 512.5 155.6 0 32 7 -threads ",
		label=threads,
		lp="512.5,157.5",
		pos="e,502.48,144.26 481.62,178.58 486.09,171.23 492.69,160.37 498.1,151.46"];
	fastqc	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 613.5 125.5 613.5 144.5 863.5 144.5 863.5 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 738.5 132.5 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="738.5,135",
		rects="613.5,125.5,863.5,144.5",
		width=3.4722];
	threads -> fastqc	[_draw_="c 7 -#000000 B 13 516.22 178.56 530.74 175.63 547.33 172.46 562.5 170 590.36 165.48 597.78 167.3 625.5 162 641.28 158.98 644.87 \
156.71 660.5 153 670.09 150.72 680.36 148.4 690.21 146.23 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 690.56 148.66 696.88 144.77 689.51 143.88 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 676.5 155.6 0 32 7 -threads ",
		label=threads,
		lp="676.5,157.5",
		pos="e,698.35,144.45 516.22,178.56 530.74,175.63 547.33,172.46 562.5,170 590.36,165.48 597.78,167.3 625.5,162 641.28,158.98 644.87,156.71 \
660.5,153 670.09,150.72 680.36,148.4 690.21,146.23"];
	fastq_dir -> "salmon-bulk-mouse"	[_draw_="c 7 -#000000 B 10 597.97 178.52 580.29 174.66 560.64 169.28 543.5 162 536.69 159.11 536.53 155.31 529.5 153 505.22 145.01 443.22 \
146.72 406.98 144.98 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 407.44 142.56 400.31 144.58 407.15 147.45 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 561.5 155.6 0 36 9 -fastq_dir ",
		label=fastq_dir,
		lp="561.5,157.5",
		pos="e,398.8,144.49 597.97,178.52 580.29,174.66 560.64,169.28 543.5,162 536.69,159.11 536.53,155.31 529.5,153 505.22,145.01 443.22,146.72 \
406.98,144.98"];
	fastq_dir -> "salmon-bulk"	[_draw_="c 7 -#000000 B 10 626.99 178.53 616.26 174.14 603.42 168.37 592.5 162 586.74 158.64 586.54 155.82 580.5 153 575.43 150.64 570 148.59 \
564.48 146.81 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 565.21 144.48 557.81 144.84 563.82 149.17 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 610.5 155.6 0 36 9 -fastq_dir ",
		label=fastq_dir,
		lp="610.5,157.5",
		pos="e,556.36,144.41 626.99,178.53 616.26,174.14 603.42,168.37 592.5,162 586.74,158.64 586.54,155.82 580.5,153 575.43,150.64 570,148.59 \
564.48,146.81"];
	fastq_dir -> fastqc	[_draw_="c 7 -#000000 B 4 664.2 178.58 678.5 170.38 700.4 157.83 716.72 148.48 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 717.61 150.79 722.47 145.19 715.18 146.54 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 724.5 155.6 0 36 9 -fastq_dir ",
		label=fastq_dir,
		lp="724.5,157.5",
		pos="e,723.78,144.43 664.2,178.58 678.5,170.38 700.4,157.83 716.72,148.48"];
	organism -> "salmon-bulk-mouse"	[_draw_="c 7 -#000000 B 4 349.59 178.58 340.33 170.71 326.34 158.82 315.5 149.6 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 317.3 147.91 310.38 145.25 314.12 151.65 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 349 155.6 0 39 8 -organism ",
		label=organism,
		lp="349,157.5",
		pos="e,309.22,144.26 349.59,178.58 340.33,170.71 326.34,158.82 315.5,149.6"];
	organism -> "salmon-bulk"	[_draw_="c 7 -#000000 B 13 374.83 178.53 380.82 175.49 387.85 172.26 394.5 170 411.26 164.31 416.78 167.78 433.5 162 441.95 159.08 443.19 \
156.31 451.5 153 456.95 150.83 462.79 148.77 468.57 146.89 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 468.98 149.33 474.92 144.89 467.51 144.65 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 471 155.6 0 39 8 -organism ",
		label=organism,
		lp="471,157.5",
		pos="e,476.37,144.43 374.83,178.53 380.82,175.49 387.85,172.26 394.5,170 411.26,164.31 416.78,167.78 433.5,162 441.95,159.08 443.19,156.31 \
451.5,153 456.95,150.83 462.79,148.77 468.57,146.89"];
	make_expression_matrix	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 0 80.5 0 99.5 555 99.5 555 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 277.5 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="277.5,90",
		rects="0,80.5,555,99.5",
		width=7.7083];
	"salmon-bulk-mouse" -> make_expression_matrix	[_draw_="c 7 -#000000 B 4 295.26 125.71 292.52 120.36 288.87 113.22 285.59 106.81 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 287.79 105.73 282.42 100.61 283.43 107.96 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 309 110.6 0 39 9 -quant_dir ",
		label=quant_dir,
		lp="309,112.5",
		pos="e,281.73,99.265 295.26,125.71 292.52,120.36 288.87,113.22 285.59,106.81"];
	"salmon-bulk" -> salmon_output	[_draw_="c 7 -#000000 B 7 525.96 125.67 536.38 119.97 548.66 111.38 555.5 100 562.2 88.86 563.72 74.11 563.7 62.84 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 566.15 62.77 563.44 55.86 561.25 62.94 ",
		pos="e,563.39,54.348 525.96,125.67 536.38,119.97 548.66,111.38 555.5,100 562.2,88.863 563.72,74.111 563.7,62.84"];
	"salmon-bulk" -> make_expression_matrix	[_draw_="c 7 -#000000 B 4 462.06 125.5 424.41 118.47 370.84 108.45 331.1 101.02 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 331.67 98.63 324.33 99.76 330.76 103.45 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 432 110.6 0 39 9 -quant_dir ",
		label=quant_dir,
		lp="432,112.5",
		pos="e,322.85,99.478 462.06,125.5 424.41,118.47 370.84,108.45 331.1,101.02"];
	fastqc -> fastqc_dir	[_draw_="c 7 -#000000 B 4 746.07 125.56 759.56 110.54 787.86 79.01 804.51 60.47 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 806.2 62.26 809.05 55.41 802.55 58.98 ",
		pos="e,810.06,54.284 746.07,125.56 759.56,110.54 787.86,79.013 804.51,60.472"];
	make_expression_matrix -> expression_matrix	[_draw_="c 7 -#000000 B 4 276.92 80.71 276.56 75.59 276.09 68.85 275.66 62.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 278.11 62.59 275.18 55.78 273.23 62.93 ",
		pos="e,275.08,54.265 276.92,80.709 276.56,75.593 276.09,68.848 275.66,62.666"];
}
