From ae799bc0c2e5aeaa9e7e3500f06ad07ab55c31b8 Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus <brilhaus@nfdi4plants.org> Date: Fri, 28 Mar 2025 10:13:56 +0100 Subject: [PATCH] add workflow plots --- runs/deseq2/run.svg | 101 ++++++++++++++++++ runs/fastqc/run.svg | 65 ++++++++++++ runs/isaSampleToRawDataSeq/run.svg | 101 ++++++++++++++++++ runs/kallisto/run.svg | 125 ++++++++++++++++++++++ runs/shiny/run.svg | 48 +++++++++ runs/sleuth/run.svg | 113 ++++++++++++++++++++ workflows/deseq2/workflow.svg | 125 ++++++++++++++++++++++ workflows/fastqc/workflow.svg | 83 +++++++++++++++ workflows/kallisto/workflow.svg | 161 +++++++++++++++++++++++++++++ workflows/sleuth/workflow.svg | 149 ++++++++++++++++++++++++++ 10 files changed, 1071 insertions(+) create mode 100644 runs/deseq2/run.svg create mode 100644 runs/fastqc/run.svg create mode 100644 runs/isaSampleToRawDataSeq/run.svg create mode 100644 runs/kallisto/run.svg create mode 100644 runs/shiny/run.svg create mode 100644 runs/sleuth/run.svg create mode 100644 workflows/deseq2/workflow.svg create mode 100644 workflows/fastqc/workflow.svg create mode 100644 workflows/kallisto/workflow.svg create mode 100644 workflows/sleuth/workflow.svg diff --git a/runs/deseq2/run.svg b/runs/deseq2/run.svg new file mode 100644 index 0000000..6e83131 --- /dev/null +++ b/runs/deseq2/run.svg @@ -0,0 +1,101 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" + "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> +<!-- Generated by graphviz version 9.0.0 (0) + --> +<!-- Title: G Pages: 1 --> +<svg width="655pt" height="251pt" + viewBox="0.00 0.00 655.00 251.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"> +<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 247)"> +<title>G</title> +<polygon fill="#eeeeee" stroke="none" points="-4,4 -4,-247 651,-247 651,4 -4,4"/> +<g id="clust1" class="cluster"> +<title>cluster_inputs</title> +<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="8,-157.5 8,-235 639,-235 639,-157.5 8,-157.5"/> +<text text-anchor="middle" x="584.5" y="-164.7" font-family="Times,serif" font-size="14.00">Workflow Inputs</text> +</g> +<g id="clust2" class="cluster"> +<title>cluster_outputs</title> +<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="277,-8 277,-85.5 395,-85.5 395,-8 277,-8"/> +<text text-anchor="middle" x="336" y="-15.2" font-family="Times,serif" font-size="14.00">Workflow Outputs</text> +</g> +<!-- resultsoutdir --> +<g id="node1" class="node"> +<title>resultsoutdir</title> +<polygon fill="#94ddf4" stroke="black" points="547.25,-190.5 547.25,-226.5 630.75,-226.5 630.75,-190.5 547.25,-190.5"/> +<text text-anchor="middle" x="589" y="-203.45" font-family="Times,serif" font-size="14.00">resultsoutdir</text> +</g> +<!-- deseq2 --> +<g id="node6" class="node"> +<title>deseq2</title> +<ellipse fill="none" stroke="black" cx="336" cy="-131.5" rx="36.51" ry="18"/> +<text text-anchor="middle" x="336" y="-126.45" font-family="Times,serif" font-size="14.00">deseq2</text> +</g> +<!-- resultsoutdir->deseq2 --> +<g id="edge1" class="edge"> +<title>resultsoutdir->deseq2</title> +<path fill="none" stroke="black" d="M576.63,-190.16C567.57,-178.88 554.23,-164.93 539,-157.5 512.5,-144.57 434.96,-137.9 383.75,-134.8"/> +<polygon fill="black" stroke="black" points="383.99,-131.31 373.81,-134.23 383.59,-138.3 383.99,-131.31"/> +</g> +<!-- inKallistoResults --> +<g id="node2" class="node"> +<title>inKallistoResults</title> +<polygon fill="#94ddf4" stroke="black" points="420.5,-190.5 420.5,-226.5 529.5,-226.5 529.5,-190.5 420.5,-190.5"/> +<text text-anchor="middle" x="475" y="-203.45" font-family="Times,serif" font-size="14.00">inKallistoResults</text> +</g> +<!-- inKallistoResults->deseq2 --> +<g id="edge2" class="edge"> +<title>inKallistoResults->deseq2</title> +<path fill="none" stroke="black" d="M456.67,-190.07C444.71,-179.46 428.35,-166.31 412,-157.5 401.73,-151.96 390.02,-147.37 378.91,-143.69"/> +<polygon fill="black" stroke="black" points="380.12,-140.41 369.53,-140.78 378.04,-147.09 380.12,-140.41"/> +</g> +<!-- inMetadataFactorList --> +<g id="node3" class="node"> +<title>inMetadataFactorList</title> +<polygon fill="#94ddf4" stroke="black" points="269.5,-190.5 269.5,-226.5 402.5,-226.5 402.5,-190.5 269.5,-190.5"/> +<text text-anchor="middle" x="336" y="-203.45" font-family="Times,serif" font-size="14.00">inMetadataFactorList</text> +</g> +<!-- inMetadataFactorList->deseq2 --> +<g id="edge3" class="edge"> +<title>inMetadataFactorList->deseq2</title> +<path fill="none" stroke="black" d="M336,-190.1C336,-181.49 336,-170.87 336,-161.1"/> +<polygon fill="black" stroke="black" points="339.5,-161.31 336,-151.31 332.5,-161.31 339.5,-161.31"/> +</g> +<!-- inMetadataFile --> +<g id="node4" class="node"> +<title>inMetadataFile</title> +<polygon fill="#94ddf4" stroke="black" points="152.75,-190.5 152.75,-226.5 251.25,-226.5 251.25,-190.5 152.75,-190.5"/> +<text text-anchor="middle" x="202" y="-203.45" font-family="Times,serif" font-size="14.00">inMetadataFile</text> +</g> +<!-- inMetadataFile->deseq2 --> +<g id="edge4" class="edge"> +<title>inMetadataFile->deseq2</title> +<path fill="none" stroke="black" d="M218.99,-190.03C230.12,-179.41 245.44,-166.25 261,-157.5 270.86,-151.96 282.13,-147.39 292.9,-143.75"/> +<polygon fill="black" stroke="black" points="293.93,-147.1 302.41,-140.74 291.82,-140.42 293.93,-147.1"/> +</g> +<!-- inMetadataSample --> +<g id="node5" class="node"> +<title>inMetadataSample</title> +<polygon fill="#94ddf4" stroke="black" points="15.62,-190.5 15.62,-226.5 134.38,-226.5 134.38,-190.5 15.62,-190.5"/> +<text text-anchor="middle" x="75" y="-203.45" font-family="Times,serif" font-size="14.00">inMetadataSample</text> +</g> +<!-- inMetadataSample->deseq2 --> +<g id="edge5" class="edge"> +<title>inMetadataSample->deseq2</title> +<path fill="none" stroke="black" d="M93.37,-190.23C106.46,-178.98 125.03,-165.04 144,-157.5 190.63,-138.97 248.16,-133.55 288.02,-132.25"/> +<polygon fill="black" stroke="black" points="287.86,-135.76 297.77,-132.01 287.69,-128.76 287.86,-135.76"/> +</g> +<!-- output --> +<g id="node7" class="node"> +<title>output</title> +<polygon fill="#94ddf4" stroke="black" points="309,-41 309,-77 363,-77 363,-41 309,-41"/> +<text text-anchor="middle" x="335.75" y="-53.95" font-family="Times,serif" font-size="14.00">output</text> +</g> +<!-- deseq2->output --> +<g id="edge6" class="edge"> +<title>deseq2->output</title> +<path fill="none" stroke="black" d="M336,-113.07C336,-105.73 336,-96.99 336,-88.74"/> +<polygon fill="black" stroke="black" points="339.5,-88.74 336,-78.74 332.5,-88.74 339.5,-88.74"/> +</g> +</g> +</svg> diff --git a/runs/fastqc/run.svg b/runs/fastqc/run.svg new file mode 100644 index 0000000..55c03b4 --- /dev/null +++ b/runs/fastqc/run.svg @@ -0,0 +1,65 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" + "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> +<!-- Generated by graphviz version 9.0.0 (0) + --> +<!-- Title: G Pages: 1 --> +<svg width="193pt" height="251pt" + viewBox="0.00 0.00 193.00 251.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"> +<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 247)"> +<title>G</title> +<polygon fill="#eeeeee" stroke="none" points="-4,4 -4,-247 189,-247 189,4 -4,4"/> +<g id="clust1" class="cluster"> +<title>cluster_inputs</title> +<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="15,-157.5 15,-235 177,-235 177,-157.5 15,-157.5"/> +<text text-anchor="middle" x="122.5" y="-164.7" font-family="Times,serif" font-size="14.00">Workflow Inputs</text> +</g> +<g id="clust2" class="cluster"> +<title>cluster_outputs</title> +<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="8,-8 8,-85.5 126,-85.5 126,-8 8,-8"/> +<text text-anchor="middle" x="67" y="-15.2" font-family="Times,serif" font-size="14.00">Workflow Outputs</text> +</g> +<!-- fastq --> +<g id="node1" class="node"> +<title>fastq</title> +<polygon fill="#94ddf4" stroke="black" points="115,-190.5 115,-226.5 169,-226.5 169,-190.5 115,-190.5"/> +<text text-anchor="middle" x="141.62" y="-203.45" font-family="Times,serif" font-size="14.00">fastq</text> +</g> +<!-- fastqc --> +<g id="node3" class="node"> +<title>fastqc</title> +<ellipse fill="none" stroke="black" cx="67" cy="-131.5" rx="32.93" ry="18"/> +<text text-anchor="middle" x="67" y="-126.45" font-family="Times,serif" font-size="14.00">fastqc</text> +</g> +<!-- fastq->fastqc --> +<g id="edge1" class="edge"> +<title>fastq->fastqc</title> +<path fill="none" stroke="black" d="M131.76,-190.04C125.22,-179.81 116.09,-167.06 106,-157.5 103.78,-155.39 101.35,-153.36 98.84,-151.43"/> +<polygon fill="black" stroke="black" points="100.96,-148.64 90.76,-145.77 96.94,-154.37 100.96,-148.64"/> +</g> +<!-- finaloutdir --> +<g id="node2" class="node"> +<title>finaloutdir</title> +<polygon fill="#94ddf4" stroke="black" points="23.5,-190.5 23.5,-226.5 96.5,-226.5 96.5,-190.5 23.5,-190.5"/> +<text text-anchor="middle" x="60" y="-203.45" font-family="Times,serif" font-size="14.00">finaloutdir</text> +</g> +<!-- finaloutdir->fastqc --> +<g id="edge2" class="edge"> +<title>finaloutdir->fastqc</title> +<path fill="none" stroke="black" d="M61.62,-190.1C62.43,-181.49 63.42,-170.87 64.33,-161.1"/> +<polygon fill="black" stroke="black" points="67.8,-161.59 65.24,-151.31 60.83,-160.94 67.8,-161.59"/> +</g> +<!-- fastqc_outdir --> +<g id="node4" class="node"> +<title>fastqc_outdir</title> +<polygon fill="#94ddf4" stroke="black" points="23.38,-41 23.38,-77 110.62,-77 110.62,-41 23.38,-41"/> +<text text-anchor="middle" x="67" y="-53.95" font-family="Times,serif" font-size="14.00">fastqc_outdir</text> +</g> +<!-- fastqc->fastqc_outdir --> +<g id="edge3" class="edge"> +<title>fastqc->fastqc_outdir</title> +<path fill="none" stroke="black" d="M67,-113.07C67,-105.73 67,-96.99 67,-88.74"/> +<polygon fill="black" stroke="black" points="70.5,-88.74 67,-78.74 63.5,-88.74 70.5,-88.74"/> +</g> +</g> +</svg> diff --git a/runs/isaSampleToRawDataSeq/run.svg b/runs/isaSampleToRawDataSeq/run.svg new file mode 100644 index 0000000..86ceb3d --- /dev/null +++ b/runs/isaSampleToRawDataSeq/run.svg @@ -0,0 +1,101 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" + "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> +<!-- Generated by graphviz version 9.0.0 (0) + --> +<!-- Title: G Pages: 1 --> +<svg width="408pt" height="251pt" + viewBox="0.00 0.00 408.00 251.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"> +<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 247)"> +<title>G</title> +<polygon fill="#eeeeee" stroke="none" points="-4,4 -4,-247 404,-247 404,4 -4,4"/> +<g id="clust1" class="cluster"> +<title>cluster_inputs</title> +<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="8,-157.5 8,-235 392,-235 392,-157.5 8,-157.5"/> +<text text-anchor="middle" x="337.5" y="-164.7" font-family="Times,serif" font-size="14.00">Workflow Inputs</text> +</g> +<g id="clust2" class="cluster"> +<title>cluster_outputs</title> +<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="88,-8 88,-85.5 314,-85.5 314,-8 88,-8"/> +<text text-anchor="middle" x="255" y="-15.2" font-family="Times,serif" font-size="14.00">Workflow Outputs</text> +</g> +<!-- arcPath --> +<g id="node1" class="node"> +<title>arcPath</title> +<polygon fill="#94ddf4" stroke="black" points="327.75,-190.5 327.75,-226.5 384.25,-226.5 384.25,-190.5 327.75,-190.5"/> +<text text-anchor="middle" x="356" y="-203.45" font-family="Times,serif" font-size="14.00">arcPath</text> +</g> +<!-- isaSampleToRawDataSeq --> +<g id="node5" class="node"> +<title>isaSampleToRawDataSeq</title> +<ellipse fill="none" stroke="black" cx="202" cy="-131.5" rx="107.65" ry="18"/> +<text text-anchor="middle" x="202" y="-126.45" font-family="Times,serif" font-size="14.00">isaSampleToRawDataSeq</text> +</g> +<!-- arcPath->isaSampleToRawDataSeq --> +<g id="edge1" class="edge"> +<title>arcPath->isaSampleToRawDataSeq</title> +<path fill="none" stroke="black" d="M347.37,-190.08C341.02,-179.07 331.35,-165.45 319,-157.5 312.35,-153.22 305.1,-149.66 297.56,-146.7"/> +<polygon fill="black" stroke="black" points="298.77,-143.42 288.17,-143.4 296.45,-150.02 298.77,-143.42"/> +</g> +<!-- assayName --> +<g id="node2" class="node"> +<title>assayName</title> +<polygon fill="#94ddf4" stroke="black" points="231.88,-190.5 231.88,-226.5 310.12,-226.5 310.12,-190.5 231.88,-190.5"/> +<text text-anchor="middle" x="271" y="-203.45" font-family="Times,serif" font-size="14.00">assayName</text> +</g> +<!-- assayName->isaSampleToRawDataSeq --> +<g id="edge2" class="edge"> 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+<title>isaSampleToRawDataSeq->sampleseqCsv</title> +<path fill="none" stroke="black" d="M215.8,-113.43C222.42,-105.24 230.5,-95.25 237.88,-86.13"/> +<polygon fill="black" stroke="black" points="240.42,-88.55 243.98,-78.58 234.97,-84.15 240.42,-88.55"/> +</g> +<!-- sampleseqXlsx --> +<g id="node7" class="node"> +<title>sampleseqXlsx</title> +<polygon fill="#94ddf4" stroke="black" points="95.75,-41 95.75,-77 194.25,-77 194.25,-41 95.75,-41"/> +<text text-anchor="middle" x="145" y="-53.95" font-family="Times,serif" font-size="14.00">sampleseqXlsx</text> +</g> +<!-- isaSampleToRawDataSeq->sampleseqXlsx --> +<g id="edge6" class="edge"> +<title>isaSampleToRawDataSeq->sampleseqXlsx</title> +<path fill="none" stroke="black" d="M188.2,-113.43C181.58,-105.24 173.5,-95.25 166.12,-86.13"/> +<polygon fill="black" stroke="black" points="169.03,-84.15 160.02,-78.58 163.58,-88.55 169.03,-84.15"/> +</g> +</g> +</svg> diff --git a/runs/kallisto/run.svg b/runs/kallisto/run.svg new file mode 100644 index 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points="125.12,-77 125.12,-113 198.88,-113 198.88,-77 125.12,-77"/> +<text text-anchor="middle" x="162" y="-89.95" font-family="Times,serif" font-size="14.00">exp_factor</text> +</g> +<!-- run_shiny --> +<g id="node3" class="node"> +<title>run_shiny</title> +<ellipse fill="none" stroke="black" cx="112" cy="-18" rx="47.77" ry="18"/> +<text text-anchor="middle" x="112" y="-12.95" font-family="Times,serif" font-size="14.00">run_shiny</text> +</g> +<!-- exp_factor->run_shiny --> +<g id="edge1" class="edge"> +<title>exp_factor->run_shiny</title> +<path fill="none" stroke="black" d="M150.4,-76.6C144.19,-67.29 136.42,-55.63 129.49,-45.24"/> +<polygon fill="black" stroke="black" points="132.49,-43.42 124.03,-37.04 126.66,-47.31 132.49,-43.42"/> +</g> +<!-- in_kallisto_df --> +<g id="node2" class="node"> +<title>in_kallisto_df</title> +<polygon fill="#94ddf4" stroke="black" points="16.5,-77 16.5,-113 107.5,-113 107.5,-77 16.5,-77"/> +<text text-anchor="middle" x="62" y="-89.95" 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stroke="black" d="M146.8,-264.37C153.27,-254.97 161.43,-243.12 168.71,-232.56"/> +<polygon fill="black" stroke="black" points="171.42,-234.79 174.21,-224.57 165.65,-230.82 171.42,-234.79"/> +</g> +</g> +</svg> diff --git a/workflows/kallisto/workflow.svg b/workflows/kallisto/workflow.svg new file mode 100644 index 0000000..cba2955 --- /dev/null +++ b/workflows/kallisto/workflow.svg @@ -0,0 +1,161 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" + "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> +<!-- Generated by graphviz version 9.0.0 (0) + --> +<!-- Title: G Pages: 1 --> +<svg width="802pt" height="398pt" + viewBox="0.00 0.00 802.00 398.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"> +<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 394)"> +<title>G</title> +<polygon fill="#eeeeee" stroke="none" points="-4,4 -4,-394 798,-394 798,4 -4,4"/> +<g id="clust1" 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