digraph workflow {
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	subgraph cluster_inputs {
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		fastq_dir	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 496.5 313.5 496.5 332.5 669.5 332.5 669.5 313.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 583 320.5 0 157 32 -Directory containing FASTQ files ",
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			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 442 320.5 0 85 15 -scRNA-seq assay ",
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			rects="391.5,313.5,492.5,332.5",
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			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 867 320.5 0 148 28 -Number of threads for Salmon ",
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			pos="867,323",
			rects="785,313.5,949,332.5",
			width=2.2778];
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	subgraph cluster_outputs {
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			_ldraw_="F 10 11 -Times-Roman c 7 -#000000 T 62 15 0 92 16 -Workflow Outputs ",
			bb="8,8,1348,63",
			label="Workflow Outputs",
			labelloc=b,
			lheight=0.15,
			lp="62,17.5",
			lwidth=1.28,
			rank=same,
			style=dashed
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		raw_count_matrix	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 454 35.5 454 54.5 948 54.5 948 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 701 42.5 0 478 96 -Unfiltered count matrix from Alevin, converted to H5AD, with intronic counts \
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			label="Unfiltered count matrix from Alevin, converted to H5AD, with intronic counts as separate columns",
			pos="701,45",
			rects="454,35.5,948,54.5",
			width=6.8611];
		genome_build_json	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 952 35.5 952 54.5 1172 54.5 1172 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1062 42.5 0 204 39 -Genome build information in JSON format ",
			fillcolor="#94DDF4",
			height=0.27778,
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			pos="1062,45",
			rects="952,35.5,1172,54.5",
			width=3.0556];
		count_matrix_h5ad	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 16 35.5 16 54.5 450 54.5 450 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 233 42.5 0 418 84 -Unfiltered count matrix from Alevin, converted to H5AD, spliced and unspliced \
counts ",
			fillcolor="#94DDF4",
			height=0.27778,
			label="Unfiltered count matrix from Alevin, converted to H5AD, spliced and unspliced counts",
			pos="233,45",
			rects="16,35.5,450,54.5",
			width=6.0278];
		salmon_output	[_draw_="c 7 -#000000 C 7 -#94ddf4 P 4 1176 35.5 1176 54.5 1340 54.5 1340 35.5 ",
			_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 1258 42.5 0 148 30 -Full output of `salmon alevin` ",
			fillcolor="#94DDF4",
			height=0.27778,
			label="Full output of `salmon alevin`",
			pos="1258,45",
			rects="1176,35.5,1340,54.5",
			width=2.2778];
	}
	trim_reads	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 493.5 215.5 493.5 234.5 588.5 234.5 588.5 215.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 541 222.5 0 79 16 -Trim FASTQ files ",
		height=0.27778,
		label="Trim FASTQ files",
		pos="541,225",
		rects="493.5,215.5,588.5,234.5",
		width=1.3194];
	fastq_dir -> trim_reads	[_draw_="c 7 -#000000 B 10 590.37 313.88 594.04 309.28 598.09 303.22 600 297 605.01 280.72 600.01 273.78 590 260 583.73 251.36 574.56 244.16 \
565.84 238.65 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 567.27 236.65 560 235.19 564.78 240.87 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 631 268.1 0 60 15 -orig_fastq_dirs ",
		label=orig_fastq_dirs,
		lp="631,270",
		pos="e,558.7,234.42 590.37,313.88 594.04,309.28 598.09,303.22 600,297 605.01,280.72 600.01,273.78 590,260 583.73,251.36 574.56,244.16 \
565.84,238.65"];
	annotate_cells	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 284.5 80.5 284.5 99.5 601.5 99.5 601.5 80.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 443 87.5 0 301 63 -Assay-specific annotation of cell barcodes after quantification ",
		height=0.27778,
		label="Assay-specific annotation of cell barcodes after quantification",
		pos="443,90",
		rects="284.5,80.5,601.5,99.5",
		width=4.4028];
	fastq_dir -> annotate_cells	[_draw_="c 7 -#000000 B 10 586.55 313.51 590.4 303.52 596 286.35 596 271 596 271 596 271 596 134 596 117.78 563.71 107.38 528.8 100.89 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 529.65 98.55 522.34 99.74 528.8 103.38 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 626 200.6 0 60 15 -orig_fastq_dirs ",
		label=orig_fastq_dirs,
		lp="626,202.5",
		pos="e,520.84,99.481 586.55,313.51 590.4,303.52 596,286.35 596,271 596,271 596,271 596,134 596,117.78 563.71,107.38 528.8,100.89"];
	adjust_barcodes	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 330.5 260.5 330.5 279.5 555.5 279.5 555.5 260.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 443 267.5 0 209 42 -Assay-specific adjustment of cell barcodes ",
		height=0.27778,
		label="Assay-specific adjustment of cell barcodes",
		pos="443,270",
		rects="330.5,260.5,555.5,279.5",
		width=3.125];
	fastq_dir -> adjust_barcodes	[_draw_="c 7 -#000000 B 4 559.88 313.58 536.37 305.01 499.81 291.7 473.84 282.24 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 474.99 280.05 467.57 279.95 473.31 284.65 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 531 290.6 0 36 9 -fastq_dir ",
		label=fastq_dir,
		lp="531,292.5",
		pos="e,466.15,279.43 559.88,313.58 536.37,305.01 499.81,291.7 473.84,282.24"];
	salmon	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 621.5 170.5 621.5 189.5 828.5 189.5 828.5 170.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 725 177.5 0 191 37 -Run Salmon Alevin tool on FASTQ input ",
		height=0.27778,
		label="Run Salmon Alevin tool on FASTQ input",
		pos="725,180",
		rects="621.5,170.5,828.5,189.5",
		width=2.875];
	fastq_dir -> salmon	[_draw_="c 7 -#000000 B 10 609.85 313.64 626.98 307.03 648.43 296.19 662 280 673.11 266.75 665.7 258.16 674 243 683.83 225.05 699.16 207.3 \
710.44 195.42 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 712.06 197.27 715.18 190.55 708.55 193.86 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 704 245.6 0 60 15 -orig_fastq_dirs ",
		label=orig_fastq_dirs,
		lp="704,247.5",
		pos="e,716.24,189.46 609.85,313.64 626.98,307.03 648.43,296.19 662,280 673.11,266.75 665.7,258.16 674,243 683.83,225.05 699.16,207.3 \
710.44,195.42"];
	expected_cell_count -> salmon	[_draw_="c 7 -#000000 B 13 298.28 313.53 260.81 301.52 204.79 277.15 225 243 246.18 207.23 266.95 209.13 307 198 349.43 186.21 461 191.79 \
505 190 540.27 188.57 578.72 187 613.47 185.57 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 613.35 188.03 620.24 185.3 613.15 183.13 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 266.5 245.6 0 83 19 -expected_cell_count ",
		label=expected_cell_count,
		lp="266.5,247.5",
		pos="e,621.75,185.23 298.28,313.53 260.81,301.52 204.79,277.15 225,243 246.18,207.23 266.95,209.13 307,198 349.43,186.21 461,191.79 505,\
190 540.27,188.57 578.72,187 613.47,185.57"];
	keep_all_barcodes -> salmon	[_draw_="c 7 -#000000 B 7 728.83 313.71 731.79 299.33 737.07 268.83 735 243 733.75 227.43 730.77 209.88 728.39 197.43 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 730.85 197.25 727.08 190.86 726.04 198.2 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 773 245.6 0 76 17 -keep_all_barcodes ",
		label=keep_all_barcodes,
		lp="773,247.5",
		pos="e,726.79,189.37 728.83,313.71 731.79,299.33 737.07,268.83 735,243 733.75,227.43 730.77,209.88 728.39,197.43"];
	assay -> trim_reads	[_draw_="c 7 -#000000 B 10 469.93 313.54 502 303.56 550.86 287.37 556 280 565.44 266.47 559.34 258.23 553 243 552.76 242.42 552.5 241.85 \
552.22 241.28 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 554.43 240.19 548.68 235.5 550.25 242.75 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 572.5 268.1 0 25 5 -assay ",
		label=assay,
		lp="572.5,270",
		pos="e,547.89,234.21 469.93,313.54 502,303.56 550.86,287.37 556,280 565.44,266.47 559.34,258.23 553,243 552.76,242.42 552.5,241.85 552.22,\
241.28"];
	assay -> annotate_cells	[_draw_="c 7 -#000000 B 16 417.46 313.52 408.29 310.55 397.74 307.37 388 305 367.84 300.1 360.75 305.9 342 297 326.06 289.43 312 288.64 312 \
271 312 271 312 271 312 134 312 118.77 344.35 108.06 376.9 101.14 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 377.31 103.56 383.68 99.76 376.33 98.75 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 324.5 200.6 0 25 5 -assay ",
		label=assay,
		lp="324.5,202.5",
		pos="e,385.16,99.458 417.46,313.52 408.29,310.55 397.74,307.37 388,305 367.84,300.1 360.75,305.9 342,297 326.06,289.43 312,288.64 312,\
271 312,271 312,271 312,134 312,118.77 344.35,108.06 376.9,101.14"];
	assay -> adjust_barcodes	[_draw_="c 7 -#000000 B 4 442.17 313.58 442.3 306.52 442.51 296.24 442.68 287.55 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 445.12 287.82 442.81 280.78 440.22 287.73 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 454.5 290.6 0 25 5 -assay ",
		label=assay,
		lp="454.5,292.5",
		pos="e,442.84,279.26 442.17,313.58 442.3,306.52 442.51,296.24 442.68,287.55"];
	assay -> salmon	[_draw_="c 7 -#000000 B 10 414.55 313.51 383.05 303.49 335.04 287.28 330 280 324.94 272.69 324.81 267.22 330 260 362.57 214.65 508.18 195.14 \
613.15 186.88 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 613.28 189.32 620.08 186.35 612.91 184.44 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 358.5 245.6 0 25 5 -assay ",
		label=assay,
		lp="358.5,247.5",
		pos="e,621.59,186.23 414.55,313.51 383.05,303.49 335.04,287.28 330,280 324.94,272.69 324.81,267.22 330,260 362.57,214.65 508.18,195.14 \
613.15,186.88"];
	threads -> trim_reads	[_draw_="c 7 -#000000 B 10 857.43 313.59 849.03 305.7 837.08 293.18 830 280 821.94 264.99 833.2 253.76 820 243 803.12 229.24 672.8 226.42 \
596.38 225.96 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 596.78 223.51 589.76 225.93 596.75 228.41 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 846 268.1 0 32 7 -threads ",
		label=threads,
		lp="846,270",
		pos="e,588.25,225.92 857.43,313.59 849.03,305.7 837.08,293.18 830,280 821.94,264.99 833.2,253.76 820,243 803.12,229.24 672.8,226.42 596.38,\
225.96"];
	threads -> salmon	[_draw_="c 7 -#000000 B 7 868.11 313.59 869.33 300.87 869.88 276.49 859 260 836.17 225.4 792.55 203.89 761.27 192.21 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 762.44 190.03 755.03 189.97 760.78 194.64 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 868 245.6 0 32 7 -threads ",
		label=threads,
		lp="868,247.5",
		pos="e,753.6,189.45 868.11,313.59 869.33,300.87 869.88,276.49 859,260 836.17,225.4 792.55,203.89 761.27,192.21"];
	trim_reads -> salmon	[_draw_="c 7 -#000000 B 7 526.25 215.73 518.89 210.58 512.61 203.85 518 198 525.07 190.32 568.1 186.11 613.1 183.8 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 613.14 186.26 620.01 183.47 612.9 181.36 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 554.5 200.6 0 73 17 -trimmed_fastq_dir ",
		label=trimmed_fastq_dir,
		lp="554.5,202.5",
		pos="e,621.52,183.39 526.25,215.73 518.89,210.58 512.61,203.85 518,198 525.07,190.32 568.1,186.11 613.1,183.8"];
	annotate_cells -> count_matrix_h5ad	[_draw_="c 7 -#000000 B 4 401.51 80.5 367.28 73.5 318.63 63.53 282.4 56.12 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 283.24 53.79 275.89 54.78 282.25 58.59 ",
		pos="e,274.4,54.478 401.51,80.505 367.28,73.496 318.63,63.535 282.4,56.115"];
	adjust_barcodes -> trim_reads	[_draw_="c 7 -#000000 B 4 462.36 260.5 477.13 254.03 497.64 245.02 514.02 237.84 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 514.87 240.14 520.29 235.09 512.9 235.66 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 526 245.6 0 52 13 -adj_fastq_dir ",
		label=adj_fastq_dir,
		lp="526,247.5",
		pos="e,521.68,234.48 462.36,260.5 477.13,254.03 497.64,245.02 514.02,237.84"];
	adjust_barcodes -> annotate_cells	[_draw_="c 7 -#000000 B 10 443 260.76 443 252.1 443 238.09 443 226 443 226 443 226 443 134 443 125.31 443 115.63 443 107.65 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 445.45 107.76 443 100.76 440.55 107.76 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 473.5 178.1 0 61 13 -metadata_json ",
		label=metadata_json,
		lp="473.5,180",
		pos="e,443,99.243 443,260.76 443,252.1 443,238.09 443,226 443,226 443,226 443,134 443,125.31 443,115.63 443,107.65"];
	salmon -> salmon_output	[_draw_="c 7 -#000000 B 7 814.25 170.53 860.27 165.14 917.06 156.89 967 145 1065.8 121.48 1178.53 78.21 1229.87 57.56 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1230.6 59.91 1236.17 55.01 1228.76 55.37 ",
		pos="e,1237.6,54.447 814.25,170.53 860.27,165.14 917.06,156.89 967,145 1065.8,121.48 1178.5,78.212 1229.9,57.561"];
	alevin_to_anndata	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 603 125.5 603 144.5 965 144.5 965 125.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 784 132.5 0 346 68 -Convert Alevin sparse output to anndata.AnnData object, save as h5ad ",
		height=0.27778,
		label="Convert Alevin sparse output to anndata.AnnData object, save as h5ad",
		pos="784,135",
		rects="603,125.5,965,144.5",
		width=5.0278];
	salmon -> alevin_to_anndata	[_draw_="c 7 -#000000 B 4 736.66 170.5 744.9 164.5 756.12 156.32 765.57 149.43 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 766.93 151.47 771.14 145.37 764.04 147.51 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 779 155.6 0 40 10 -alevin_dir ",
		label=alevin_dir,
		lp="779,157.5",
		pos="e,772.37,144.48 736.66,170.5 744.9,164.5 756.12,156.32 765.57,149.43"];
	alevin_to_anndata -> raw_count_matrix	[_draw_="c 7 -#000000 B 4 776.04 125.56 761.88 110.54 732.14 79.01 714.65 60.47 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 716.44 58.8 709.85 55.38 712.87 62.16 ",
		pos="e,708.81,54.284 776.04,125.56 761.88,110.54 732.14,79.013 714.65,60.472"];
	alevin_to_anndata -> genome_build_json	[_draw_="c 7 -#000000 B 4 810.66 125.56 861.3 109.53 971.38 74.68 1027.54 56.91 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1028.05 59.32 1033.98 54.87 1026.57 54.65 ",
		pos="e,1035.4,54.412 810.66,125.56 861.3,109.53 971.38,74.685 1027.5,56.907"];
	alevin_to_anndata -> annotate_cells	[_draw_="c 7 -#000000 B 7 727.28 125.5 690.94 120.17 642.74 113.33 600 108 578.77 105.35 555.9 102.74 534.35 100.38 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 534.9 97.98 527.67 99.66 534.37 102.85 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 684 110.6 0 38 9 -h5ad_file ",
		label=h5ad_file,
		lp="684,112.5",
		pos="e,526.17,99.496 727.28,125.5 690.94,120.17 642.74,113.33 600,108 578.77,105.35 555.9,102.74 534.35,100.38"];
}