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<text text-anchor="start" x="523" y="-2263.8" font-family="sans" font-weight="bold" font-size="14.00">output →</text>
<text text-anchor="start" x="593" y="-2263.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="254" y="-2244" font-family="monospace" font-size="10.00">results/star_alignment/bulk/{s}/{s}_GDC38.Aligned.out.bam</text>
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<!-- 3&#45;&gt;2 -->
<g id="edge5" class="edge">
<title>3&#45;&gt;2</title>
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<!-- 4 -->
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<title>4</title>
<text text-anchor="start" x="274" y="-2558.6" font-family="sans" font-weight="bold" font-size="18.00">bam_to_fastq</text>
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<text text-anchor="start" x="173" y="-2534.8" font-family="sans" font-weight="bold" font-size="14.00">↪ input</text>
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<text text-anchor="start" x="169" y="-2515" font-family="monospace" font-size="10.00">samples/bulk/{s}.Aligned.sortedByCoord.out.patched.md.bam</text>
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<text text-anchor="start" x="438" y="-2494.8" font-family="sans" font-weight="bold" font-size="14.00">output →</text>
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<text text-anchor="start" x="169" y="-2475" font-family="monospace" font-size="10.00">samples/bulk/{s}/{s}_original_R1.fastq</text>
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<!-- 4&#45;&gt;3 -->
<g id="edge7" class="edge">
<title>4&#45;&gt;3</title>
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<!-- 5 -->
<g id="node6" class="node">
<title>5</title>
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<text text-anchor="start" x="548" y="-2534.8" font-family="sans" font-weight="bold" font-size="14.00">↪ input</text>
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<text text-anchor="start" x="544" y="-2515" font-family="monospace" font-size="10.00">refs/downloads/gencode.v38.annotation.gtf.gz</text>
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<text text-anchor="start" x="735" y="-2476.8" font-family="sans" font-weight="bold" font-size="14.00">output →</text>
<text text-anchor="start" x="805" y="-2476.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="544" y="-2457" font-family="monospace" font-size="10.00">refs/index.star/genome</text>
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<!-- 5&#45;&gt;3 -->
<g id="edge6" class="edge">
<title>5&#45;&gt;3</title>
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<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
<text text-anchor="start" x="766" y="-2381.6" font-family="sans" font-weight="bold" font-size="18.00">starsolo_alignment</text>
<text text-anchor="start" x="651" y="-2357.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="655" y="-2357.8" font-family="sans" font-weight="bold" font-size="14.00">↪ input</text>
<text text-anchor="start" x="713" y="-2357.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="651" y="-2338" font-family="monospace" font-size="10.00">refs/index.star/genome</text>
<text text-anchor="start" x="651" y="-2320" font-family="monospace" font-size="10.00">resources/whitelist/whitelist.10x.v2.txt</text>
<text text-anchor="start" x="651" y="-2302" font-family="monospace" font-size="10.00">samples/single_cell_merged/{s}.bc.fastq.gz</text>
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<text text-anchor="start" x="998" y="-2263.8" font-family="sans" font-weight="bold" font-size="14.00">output →</text>
<text text-anchor="start" x="1068" y="-2263.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="651" y="-2244" font-family="monospace" font-size="10.00">results/starsolo_alignment/{s}/{s}.Aligned.sortedByCoord.out.bam</text>
<text text-anchor="start" x="651" y="-2226" font-family="monospace" font-size="10.00">results/starsolo_alignment/{s}/{s}.Solo.out/Gene/filtered/barcodes.tsv</text>
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<!-- 5&#45;&gt;12 -->
<g id="edge18" class="edge">
<title>5&#45;&gt;12</title>
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<g id="node7" class="node">
<title>6</title>
<text text-anchor="start" x="305" y="-2753.6" font-family="sans" font-weight="bold" font-size="18.00">extract_genome</text>
<text text-anchor="start" x="271" y="-2729.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="275" y="-2729.8" font-family="sans" font-weight="bold" font-size="14.00">↪ input</text>
<text text-anchor="start" x="333" y="-2729.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="271" y="-2710" font-family="monospace" font-size="10.00">refs/downloads/GRCh38.d1.vd1.fa.tar.gz</text>
<text text-anchor="start" x="422" y="-2689.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="426" y="-2689.8" font-family="sans" font-weight="bold" font-size="14.00">output →</text>
<text text-anchor="start" x="496" y="-2689.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="271" y="-2670" font-family="monospace" font-size="10.00">refs/sequences/genome.dict</text>
<text text-anchor="start" x="271" y="-2652" font-family="monospace" font-size="10.00">refs/sequences/genome.fa.gz</text>
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<!-- 6&#45;&gt;5 -->
<g id="edge8" class="edge">
<title>6&#45;&gt;5</title>
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<g id="node9" class="node">
<title>8</title>
<text text-anchor="start" x="7" y="-2354.6" font-family="sans" font-weight="bold" font-size="18.00">telescope_annotation</text>
<text text-anchor="start" x="7" y="-2330.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="11" y="-2330.8" font-family="sans" font-weight="bold" font-size="14.00">↪ input</text>
<text text-anchor="start" x="69" y="-2330.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="7" y="-2311" font-family="monospace" font-size="10.00">refs/downloads/retro.hg38.v1.gtf</text>
<text text-anchor="start" x="7" y="-2293" font-family="monospace" font-size="10.00">refs/sequences/genome.fa.gz.fai</text>
<text text-anchor="start" x="143" y="-2272.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="147" y="-2272.8" font-family="sans" font-weight="bold" font-size="14.00">output →</text>
<text text-anchor="start" x="217" y="-2272.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="7" y="-2253" font-family="monospace" font-size="10.00">refs/annotation/retro.gtf</text>
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<!-- 6&#45;&gt;8 -->
<g id="edge11" class="edge">
<title>6&#45;&gt;8</title>
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<!-- 7 -->
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<title>7</title>
<text text-anchor="start" x="296" y="-2881.6" font-family="sans" font-weight="bold" font-size="18.00">download_remote</text>
<text text-anchor="start" x="296" y="-2860" font-family="sans" font-size="10.00"> &#160;</text>
<text text-anchor="start" x="396" y="-2839.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="400" y="-2839.8" font-family="sans" font-weight="bold" font-size="14.00">output →</text>
<text text-anchor="start" x="470" y="-2839.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="296" y="-2820" font-family="monospace" font-size="10.00">refs/downloads/{f}</text>
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<!-- 7&#45;&gt;5 -->
<g id="edge9" class="edge">
<title>7&#45;&gt;5</title>
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<!-- 7&#45;&gt;6 -->
<g id="edge10" class="edge">
<title>7&#45;&gt;6</title>
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<title>7&#45;&gt;8</title>
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<g id="edge4" class="edge">
<title>8&#45;&gt;2</title>
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<!-- 10 -->
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<title>10</title>
<text text-anchor="start" x="548.5" y="-1955.6" font-family="sans" font-weight="bold" font-size="18.00">stellarscope_assign</text>
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<text text-anchor="start" x="368" y="-1931.8" font-family="sans" font-weight="bold" font-size="14.00">↪ input</text>
<text text-anchor="start" x="426" y="-1931.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="364" y="-1912" font-family="monospace" font-size="10.00">refs/annotation/retro.gtf</text>
<text text-anchor="start" x="364" y="-1894" font-family="monospace" font-size="10.00">results/starsolo_alignment/{s}/{s}.Aligned.sortedByCB.bam</text>
<text text-anchor="start" x="364" y="-1876" font-family="monospace" font-size="10.00">results/starsolo_alignment/{s}/{s}.Solo.out/Gene/filtered/barcodes.tsv</text>
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<text text-anchor="start" x="855" y="-1855.8" font-family="sans" font-weight="bold" font-size="14.00">output →</text>
<text text-anchor="start" x="925" y="-1855.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="364" y="-1836" font-family="monospace" font-size="10.00">results/stellarscope_{s_method,pseudobulk|individual}/{s}/{s}_{s_method}&#45;TE_counts.mtx</text>
<text text-anchor="start" x="364" y="-1818" font-family="monospace" font-size="10.00">results/stellarscope_{s_method,pseudobulk|individual}/{s}/{s}_{s_method}&#45;TE_counts_all.mtx</text>
<text text-anchor="start" x="364" y="-1800" font-family="monospace" font-size="10.00">results/stellarscope_{s_method,pseudobulk|individual}/{s}/{s}_{s_method}&#45;TE_counts_average.mtx</text>
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<title>9</title>
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<text text-anchor="start" x="452" y="-1637.8" font-family="sans" font-weight="bold" font-size="14.00">↪ input</text>
<text text-anchor="start" x="510" y="-1637.8" font-family="sans" font-size="10.00"> </text>
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<text text-anchor="start" x="448" y="-1600" font-family="monospace" font-size="10.00">results/stellarscope_{s_method}/{s}/{s}_{s_method}&#45;TE_counts_all.mtx</text>
<text text-anchor="start" x="448" y="-1582" font-family="monospace" font-size="10.00">results/stellarscope_{s_method}/{s}/{s}_{s_method}&#45;TE_counts_average.mtx</text>
<text text-anchor="start" x="448" y="-1564" font-family="monospace" font-size="10.00">results/stellarscope_{s_method}/{s}/{s}_{s_method}&#45;TE_counts_choose.mtx</text>
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<text text-anchor="start" x="448" y="-1528" font-family="monospace" font-size="10.00">results/stellarscope_{s_method}/{s}/{s}_{s_method}&#45;TE_counts_exclude.mtx</text>
<text text-anchor="start" x="448" y="-1510" font-family="monospace" font-size="10.00">results/stellarscope_{s_method}/{s}/{s}_{s_method}&#45;TE_counts_unique.mtx</text>
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<text text-anchor="start" x="807" y="-1489.8" font-family="sans" font-weight="bold" font-size="14.00">output →</text>
<text text-anchor="start" x="877" y="-1489.8" font-family="sans" font-size="10.00"> </text>
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<text text-anchor="start" x="675" y="-2117.8" font-family="sans" font-weight="bold" font-size="14.00">↪ input</text>
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<text text-anchor="start" x="671" y="-2080" font-family="monospace" font-size="10.00">results/starsolo_alignment/{s}/{s}.Solo.out/Gene/filtered/barcodes.tsv</text>
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<text text-anchor="start" x="1018" y="-2059.8" font-family="sans" font-weight="bold" font-size="14.00">output →</text>
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<title>13</title>
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<text text-anchor="start" x="845" y="-2543.8" font-family="sans" font-weight="bold" font-size="14.00">↪ input</text>
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<text text-anchor="start" x="841" y="-2524" font-family="monospace" font-size="10.00">&lt;input function&gt;</text>
<text text-anchor="start" x="841" y="-2506" font-family="monospace" font-size="10.00">&lt;input function&gt;</text>
<text text-anchor="start" x="1028" y="-2485.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="1032" y="-2485.8" font-family="sans" font-weight="bold" font-size="14.00">output →</text>
<text text-anchor="start" x="1102" y="-2485.8" font-family="sans" font-size="10.00"> </text>
<text text-anchor="start" x="841" y="-2466" font-family="monospace" font-size="10.00">samples/single_cell_merged/{s}.bc.fastq.gz</text>
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