digraph workflow {
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	annotate_cells	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 802.21 99.5 802.21 118.5 1119.21 118.5 1119.21 99.5 ",
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	img_dir -> annotate_cells	[_draw_="c 7 -#000000 B 10 999.02 287.8 1009.34 278.59 1023.71 262.61 1023.71 245 1023.71 245 1023.71 245 1023.71 153 1023.71 138.47 1012.14 \
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	alevin_to_anndata	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 432.71 144.5 432.71 163.5 794.71 163.5 794.71 144.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 613.71 151.5 0 346 68 -Convert Alevin sparse output to anndata.AnnData object, save as h5ad ",
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		pos="613.71,154",
		rects="432.71,144.5,794.71,163.5",
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	assay -> alevin_to_anndata	[_draw_="c 7 -#000000 B 7 829.29 287.8 841.26 275.37 860.17 251.36 847.71 234 820.05 195.47 772.61 175.49 727.64 165.22 ",
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	"salmon-mouse"	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 268.21 189.5 268.21 208.5 475.21 208.5 475.21 189.5 ",
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	assay -> "salmon-mouse"	[_draw_="c 7 -#000000 B 19 816.96 287.7 813.33 280.32 807.27 269.55 799.71 262 794.91 257.21 790.96 259.28 786.71 254 780.8 246.66 786.88 \
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	adjust_barcodes	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 1032.21 287.5 1032.21 306.5 1257.21 306.5 1257.21 287.5 ",
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		width=3.125];
	assay -> adjust_barcodes	[_draw_="c 7 -#000000 B 10 826.42 306.25 835.16 319.38 853.21 342.9 875.71 352.25 936.86 377.66 960.02 366.43 1024.71 352.25 1060.94 344.31 \
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	assay -> annotate_cells	[_draw_="c 7 -#000000 B 10 830.4 287.55 835.84 282.76 842.72 276.62 848.71 271 877.37 244.13 888.67 240.82 911.71 209 931.09 182.22 946.59 \
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	trim_reads	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 684.21 234.5 684.21 253.5 779.21 253.5 779.21 234.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 731.71 241.5 0 79 16 -Trim FASTQ files ",
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		label="Trim FASTQ files",
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		rects="684.21,234.5,779.21,253.5",
		width=1.3194];
	assay -> trim_reads	[_draw_="c 7 -#000000 B 4 806.01 287.58 791.71 279.38 769.81 266.83 753.49 257.48 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 755.03 255.54 747.74 254.19 752.59 259.79 ",
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		pos="e,746.43,253.43 806.01,287.58 791.71,279.38 769.81,266.83 753.49,257.48"];
	salmon	[_draw_="c 7 -#000000 C 7 -#fafad2 P 4 479.21 189.5 479.21 208.5 686.21 208.5 686.21 189.5 ",
		_ldraw_="F 10 9 -Helvetica c 7 -#000000 T 582.71 196.5 0 191 37 -Run Salmon Alevin tool on FASTQ input ",
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		pos="582.71,199",
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		width=2.875];
	assay -> salmon	[_draw_="c 7 -#000000 B 7 822.31 287.59 824.31 274.42 825.98 248.92 812.71 234 796.57 215.86 744.81 207.26 694.46 203.24 ",
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		label=assay,
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		pos="e,686.08,202.61 822.31,287.59 824.31,274.42 825.98,248.92 812.71,234 796.57,215.86 744.81,207.26 694.46,203.24"];
	fastq_dir -> "salmon-mouse"	[_draw_="c 7 -#000000 B 13 658.35 287.57 637.76 279.77 605.56 268.44 576.71 262 562.29 258.78 522.22 263.26 510.71 254 503.37 248.1 510.64 \
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		label=orig_fastq_dirs,
		lp="540.71,244",
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	fastq_dir -> adjust_barcodes	[_draw_="c 7 -#000000 B 10 690.53 306.35 706.7 319.61 738.67 343.29 770.71 352.25 825.06 367.46 969.57 364.33 1024.71 352.25 1060.94 344.31 \
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		label=fastq_dir,
		lp="819.71,365.5",
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	fastq_dir -> annotate_cells	[_draw_="c 7 -#000000 B 10 724.38 287.55 770.87 278.32 837.98 263.57 845.71 254 863.9 231.45 836.5 214.25 850.71 189 868.78 156.87 905.97 \
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		label=orig_fastq_dirs,
		lp="880.71,199",
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	fastq_dir -> trim_reads	[_draw_="c 7 -#000000 B 7 680.14 287.75 680.96 280.18 683.26 269.11 689.71 262 691.09 260.47 692.64 259.07 694.29 257.8 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 695.23 260.11 699.84 254.29 692.61 255.96 ",
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		label=orig_fastq_dirs,
		lp="719.71,266.5",
		pos="e,701.12,253.49 680.14,287.75 680.96,280.18 683.26,269.11 689.71,262 691.09,260.47 692.64,259.07 694.29,257.8"];
	fastq_dir -> salmon	[_draw_="c 7 -#000000 B 10 664.06 287.52 651.38 280.03 633.7 268.12 621.71 254 615.28 246.42 617.19 242.29 611.71 234 607.27 227.31 601.68 \
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		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 598.5 213.14 591.98 209.6 594.87 216.43 ",
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		label=orig_fastq_dirs,
		lp="651.71,244",
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220.47 596.6,214.69"];
	threads -> "salmon-mouse"	[_draw_="c 7 -#000000 B 7 469.52 287.55 437.73 279.6 395.33 266.99 383.71 254 374.71 243.95 371.97 228.67 371.34 216.93 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 373.79 216.91 371.22 209.95 368.89 216.99 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 399.71 242.1 0 32 7 -threads ",
		label=threads,
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	threads -> trim_reads	[_draw_="c 7 -#000000 B 7 541.82 287.55 571.16 280.54 614.11 270.4 651.71 262 661.77 259.75 672.55 257.41 682.85 255.21 ",
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		label=threads,
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	threads -> salmon	[_draw_="c 7 -#000000 B 7 528.12 287.51 542.66 280.64 561.1 269.53 571.71 254 579.2 243.03 581.8 228.07 582.61 216.68 ",
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	organism -> alevin_to_anndata	[_draw_="c 7 -#000000 B 10 126.86 296.89 99.42 296.17 59.46 291.23 31.71 271 10.33 255.42 -10.96 236.68 6.71 217 34.5 186.04 256.77 169.73 \
424.36 161.75 ",
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		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 26.21 219.6 0 39 8 -organism ",
		label=organism,
		lp="26.207,221.5",
		pos="e,432.8,161.35 126.86,296.89 99.421,296.17 59.463,291.23 31.707,271 10.334,255.42 -10.96,236.68 6.7071,217 34.499,186.04 256.77,\
169.73 424.36,161.75"];
	organism -> "salmon-mouse"	[_draw_="c 7 -#000000 B 7 127.05 292.58 81.22 286.22 3.04 269.83 30.71 234 44.76 215.8 166.18 207.18 260.18 203.21 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 260.2 205.66 267.1 202.93 260 200.77 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 50.21 242.1 0 39 8 -organism ",
		label=organism,
		lp="50.207,244",
		pos="e,268.61,202.86 127.05,292.58 81.219,286.22 3.0419,269.83 30.707,234 44.759,215.8 166.18,207.18 260.18,203.21"];
	organism -> salmon	[_draw_="c 7 -#000000 B 7 155.46 287.84 152.36 274.56 148.62 248.31 162.71 234 185.82 210.52 413.98 211.3 473.51 208.92 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 473.45 211.37 480.31 208.56 473.19 206.48 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 182.21 242.1 0 39 8 -organism ",
		label=organism,
		lp="182.21,244",
		pos="e,481.82,208.49 155.46,287.84 152.36,274.56 148.62,248.31 162.71,234 185.82,210.52 413.98,211.3 473.51,208.92"];
	metadata_dir -> annotate_cells	[_draw_="c 7 -#000000 B 13 934.25 287.65 941.23 283.53 948.75 277.94 953.71 271 960.66 261.26 960.71 256.97 960.71 245 960.71 245 960.71 \
245 960.71 153 960.71 144.31 960.71 134.63 960.71 126.65 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 963.16 126.76 960.71 119.76 958.26 126.76 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 988.21 197.1 0 55 12 -metadata_dir ",
		label=metadata_dir,
		lp="988.21,199",
		pos="e,960.71,118.24 934.25,287.65 941.23,283.53 948.75,277.94 953.71,271 960.66,261.26 960.71,256.97 960.71,245 960.71,245 960.71,245 \
960.71,153 960.71,144.31 960.71,134.63 960.71,126.65"];
	expected_cell_count -> "salmon-mouse"	[_draw_="c 7 -#000000 B 10 331.81 287.51 321.88 284.79 310.83 281.76 300.71 279 256.8 267.01 179.99 269.32 208.71 234 217.96 222.62 245.47 \
214.92 275.31 209.77 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 275.36 212.25 281.87 208.7 274.56 207.42 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 250.21 242.1 0 83 19 -expected_cell_count ",
		label=expected_cell_count,
		lp="250.21,244",
		pos="e,283.36,208.45 331.81,287.51 321.88,284.79 310.83,281.76 300.71,279 256.8,267.01 179.99,269.32 208.71,234 217.96,222.62 245.47,\
214.92 275.31,209.77"];
	expected_cell_count -> salmon	[_draw_="c 7 -#000000 B 10 374.92 287.74 385.78 279.95 401.63 267.49 412.71 254 419.14 246.16 415.57 240.05 423.71 234 438.05 223.34 455.02 \
215.87 472.44 210.67 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 472.93 213.08 479.01 208.84 471.61 208.36 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 465.21 242.1 0 83 19 -expected_cell_count ",
		label=expected_cell_count,
		lp="465.21,244",
		pos="e,480.47,208.43 374.92,287.74 385.78,279.95 401.63,267.49 412.71,254 419.14,246.16 415.57,240.05 423.71,234 438.05,223.34 455.02,\
215.87 472.44,210.67"];
	keep_all_barcodes -> "salmon-mouse"	[_draw_="c 7 -#000000 B 10 219.07 287.51 209.49 284.67 198.66 281.58 188.71 279 137.17 265.66 42.37 273.82 77.71 234 90.03 220.12 182.09 \
211.08 259.96 205.83 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 260.08 208.28 266.9 205.37 259.76 203.39 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 115.71 242.1 0 76 17 -keep_all_barcodes ",
		label=keep_all_barcodes,
		lp="115.71,244",
		pos="e,268.41,205.27 219.07,287.51 209.49,284.67 198.66,281.58 188.71,279 137.17,265.66 42.373,273.82 77.707,234 90.026,220.12 182.09,\
211.08 259.96,205.83"];
	keep_all_barcodes -> salmon	[_draw_="c 7 -#000000 B 10 257.1 287.53 266.32 279.61 279.69 267.07 288.71 254 294.24 245.98 289.86 239.78 297.71 234 305.39 228.34 406 217.28 \
485.52 209.3 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 485.41 211.78 492.13 208.64 484.92 206.9 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 335.71 242.1 0 76 17 -keep_all_barcodes ",
		label=keep_all_barcodes,
		lp="335.71,244",
		pos="e,493.64,208.49 257.1,287.53 266.32,279.61 279.69,267.07 288.71,254 294.24,245.98 289.86,239.78 297.71,234 305.39,228.34 406,217.28 \
485.52,209.3"];
	alevin_to_anndata -> raw_count_matrix	[_draw_="c 7 -#000000 B 7 642.51 144.59 679.22 133.9 744.63 114.91 800.71 99 828.52 91.11 859.95 82.35 883.94 75.7 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 884.55 78.08 890.64 73.85 883.24 73.36 ",
		pos="e,892.1,73.445 642.51,144.59 679.22,133.9 744.63,114.91 800.71,99 828.52,91.108 859.95,82.353 883.94,75.704"];
	alevin_to_anndata -> genome_build_json	[_draw_="c 7 -#000000 B 4 608.72 144.56 600 129.81 581.87 99.11 570.84 80.46 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 573.04 79.37 567.37 74.59 568.82 81.86 ",
		pos="e,566.6,73.284 608.72,144.56 600,129.81 581.87,99.114 570.84,80.46"];
	alevin_to_anndata -> annotate_cells	[_draw_="c 7 -#000000 B 7 675.02 144.55 713.64 139.31 764.56 132.53 809.71 127 830.63 124.44 853.2 121.82 874.35 119.42 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 874.5 121.87 881.19 118.65 873.96 117 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 828.71 129.6 0 38 9 -h5ad_file ",
		label=h5ad_file,
		lp="828.71,131.5",
		pos="e,882.69,118.49 675.02,144.55 713.64,139.31 764.56,132.53 809.71,127 830.63,124.44 853.2,121.82 874.35,119.42"];
	"salmon-mouse" -> salmon_output	[_draw_="c 7 -#000000 B 4 371.33 189.68 370.36 168.13 367.74 110.17 366.45 81.51 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 368.91 81.71 366.15 74.83 364.02 81.93 ",
		pos="e,366.08,73.317 371.33,189.68 370.36,168.13 367.74,110.17 366.45,81.509"];
	"salmon-mouse" -> alevin_to_anndata	[_draw_="c 7 -#000000 B 4 419.52 189.5 459.29 182.44 515.97 172.37 557.83 164.93 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 558.04 167.38 564.5 163.74 557.18 162.56 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 534.71 174.6 0 40 10 -alevin_dir ",
		label=alevin_dir,
		lp="534.71,176.5",
		pos="e,565.99,163.48 419.52,189.5 459.29,182.44 515.97,172.37 557.83,164.93"];
	adjust_barcodes -> annotate_cells	[_draw_="c 7 -#000000 B 10 1131.73 287.53 1119.72 278.55 1103.71 263.18 1103.71 245 1103.71 245 1103.71 245 1103.71 153 1103.71 137.16 1071.12 \
126.64 1037.06 119.98 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1037.67 117.6 1030.34 118.73 1036.78 122.42 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 1134.21 197.1 0 61 13 -metadata_json ",
		label=metadata_json,
		lp="1134.2,199",
		pos="e,1028.9,118.45 1131.7,287.53 1119.7,278.55 1103.7,263.18 1103.7,245 1103.7,245 1103.7,245 1103.7,153 1103.7,137.16 1071.1,126.64 \
1037.1,119.98"];
	adjust_barcodes -> trim_reads	[_draw_="c 7 -#000000 B 7 1087.99 287.52 1068.01 284.65 1045.38 281.54 1024.71 279 920.54 266.22 891.82 268.61 787.34 254.47 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 787.78 252.06 780.51 253.53 787.12 256.91 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 970.71 264.6 0 52 13 -adj_fastq_dir ",
		label=adj_fastq_dir,
		lp="970.71,266.5",
		pos="e,779.02,253.33 1088,287.52 1068,284.65 1045.4,281.54 1024.7,279 920.54,266.22 891.82,268.61 787.34,254.47"];
	annotate_cells -> count_matrix_h5ad	[_draw_="c 7 -#000000 B 4 1045.66 99.5 1118.4 92.23 1222.94 81.78 1297.86 74.28 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 1297.7 76.76 1304.42 73.63 1297.21 71.89 ",
		pos="e,1305.9,73.478 1045.7,99.505 1118.4,92.231 1222.9,81.777 1297.9,74.285"];
	trim_reads -> "salmon-mouse"	[_draw_="c 7 -#000000 B 7 684.4 234.68 682.82 234.45 681.25 234.22 679.71 234 609.88 224.11 530.81 215.44 470.27 209.32 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 470.57 206.89 463.36 208.63 470.08 211.77 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 649.21 219.6 0 73 17 -trimmed_fastq_dir ",
		label=trimmed_fastq_dir,
		lp="649.21,221.5",
		pos="e,461.85,208.48 684.4,234.68 682.82,234.45 681.25,234.22 679.71,234 609.88,224.11 530.81,215.44 470.27,209.32"];
	trim_reads -> salmon	[_draw_="c 7 -#000000 B 4 702.27 234.5 678.7 227.7 645.49 218.12 620.05 210.78 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 620.94 208.48 613.54 208.9 619.58 213.19 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 707.21 219.6 0 73 17 -trimmed_fastq_dir ",
		label=trimmed_fastq_dir,
		lp="707.21,221.5",
		pos="e,612.08,208.48 702.27,234.5 678.7,227.7 645.49,218.12 620.05,210.78"];
	salmon -> salmon_output	[_draw_="c 7 -#000000 B 7 494.86 189.53 473.21 184.47 451.01 176.5 432.71 164 402.17 143.13 381.67 103.34 372.04 81.08 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 374.42 80.41 369.47 74.88 369.89 82.29 ",
		pos="e,368.89,73.487 494.86,189.53 473.21,184.47 451.01,176.5 432.71,164 402.17,143.13 381.67,103.34 372.04,81.081"];
	salmon -> alevin_to_anndata	[_draw_="c 7 -#000000 B 4 588.68 189.71 592.72 184.12 598.15 176.58 602.92 169.96 ",
		_hdraw_="S 5 -solid c 7 -#000000 C 7 -#000000 P 3 604.76 171.6 606.86 164.49 600.78 168.74 ",
		_ldraw_="F 8 9 -Helvetica c 7 -#000000 T 621.71 174.6 0 40 10 -alevin_dir ",
		label=alevin_dir,
		lp="621.71,176.5",
		pos="e,607.75,163.27 588.68,189.71 592.72,184.12 598.15,176.58 602.92,169.96"];
}