From e396ce5d2a8d91bb6c4ebac3be7eeb18caaf1f61 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Fri, 28 Mar 2025 10:17:36 +0100
Subject: [PATCH] add back overview fig
---
.cwl/README.md | 2 +-
arc-cwl.svg | 245 +++++++++++++++++++++++++++++++++++++++++++++++++
arc.cwl | 4 +-
3 files changed, 248 insertions(+), 3 deletions(-)
create mode 100644 arc-cwl.svg
diff --git a/.cwl/README.md b/.cwl/README.md
index 6b3f620..1cb5d10 100644
--- a/.cwl/README.md
+++ b/.cwl/README.md
@@ -88,5 +88,5 @@ cwltool --parallel --timestamp run.cwl run.yml > $(date +"%Y-%m-%d_%H-%M")-run.l
### Print workflow to file
```bash
-cwltool --print-dot ../arc.cwl | dot -Tsvg > arc-cwl.svg
+cwltool --print-dot arc.cwl | dot -Tsvg > arc-cwl.svg
```
diff --git a/arc-cwl.svg b/arc-cwl.svg
new file mode 100644
index 0000000..8269aa8
--- /dev/null
+++ b/arc-cwl.svg
@@ -0,0 +1,245 @@
+<?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="2781pt" height="325pt"
+ viewBox="0.00 0.00 2781.00 325.00" 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(4 321)">
+<title>G</title>
+<polygon fill="#eeeeee" stroke="none" points="-4,4 -4,-321 2777,-321 2777,4 -4,4"/>
+<g id="clust1" class="cluster">
+<title>cluster_inputs</title>
+<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="8,-231.5 8,-309 2765,-309 2765,-231.5 8,-231.5"/>
+<text text-anchor="middle" x="2710.5" y="-238.7" 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="2217,-8 2217,-85.5 2335,-85.5 2335,-8 2217,-8"/>
+<text text-anchor="middle" x="2276" y="-15.2" font-family="Times,serif" font-size="14.00">Workflow Outputs</text>
+</g>
+<!-- isaSampleToRawDataSeq -->
+<g id="node1" class="node">
+<title>isaSampleToRawDataSeq</title>
+<polygon fill="#f3cea1" stroke="black" points="563.12,-187 563.12,-223 720.88,-223 720.88,-187 563.12,-187"/>
+<text text-anchor="middle" x="642" y="-199.95" font-family="Times,serif" font-size="14.00">isaSampleToRawDataSeq</text>
+</g>
+<!-- sleuth -->
+<g id="node2" class="node">
+<title>sleuth</title>
+<polygon fill="#f3cea1" stroke="black" points="2249,-114 2249,-150 2303,-150 2303,-114 2249,-114"/>
+<text text-anchor="middle" x="2275.62" y="-126.95" font-family="Times,serif" font-size="14.00">sleuth</text>
+</g>
+<!-- isaSampleToRawDataSeq->sleuth -->
+<g id="edge1" class="edge">
+<title>isaSampleToRawDataSeq->sleuth</title>
+<path fill="none" stroke="black" d="M721.36,-200.55C1013.99,-187.84 2026.5,-143.84 2237.35,-134.68"/>
+<polygon fill="black" stroke="black" points="2237.36,-138.18 2247.2,-134.25 2237.05,-131.19 2237.36,-138.18"/>
+</g>
+<!-- outdir -->
+<g id="node19" class="node">
+<title>outdir</title>
+<polygon fill="#94ddf4" stroke="black" points="2249,-41 2249,-77 2303,-77 2303,-41 2249,-41"/>
+<text text-anchor="middle" x="2275.62" y="-53.95" font-family="Times,serif" font-size="14.00">outdir</text>
+</g>
+<!-- sleuth->outdir -->
+<g id="edge18" class="edge">
+<title>sleuth->outdir</title>
+<path fill="none" stroke="black" d="M2276,-113.81C2276,-106.23 2276,-97.1 2276,-88.54"/>
+<polygon fill="black" stroke="black" points="2279.5,-88.54 2276,-78.54 2272.5,-88.54 2279.5,-88.54"/>
+</g>
+<!-- kallisto -->
+<g id="node3" class="node">
+<title>kallisto</title>
+<polygon fill="#f3cea1" stroke="black" points="1606.12,-187 1606.12,-223 1661.88,-223 1661.88,-187 1606.12,-187"/>
+<text text-anchor="middle" x="1634" y="-199.95" font-family="Times,serif" font-size="14.00">kallisto</text>
+</g>
+<!-- kallisto->sleuth -->
+<g id="edge2" class="edge">
+<title>kallisto->sleuth</title>
+<path fill="none" stroke="black" d="M1662,-200.9C1764.43,-189.58 2118.96,-150.37 2237.24,-137.29"/>
+<polygon fill="black" stroke="black" points="2237.52,-140.78 2247.07,-136.2 2236.75,-133.82 2237.52,-140.78"/>
+</g>
+<!-- isaSampleToRawDataSeq_arcPath -->
+<g id="node4" class="node">
+<title>isaSampleToRawDataSeq_arcPath</title>
+<polygon fill="#94ddf4" stroke="black" points="773.5,-264.5 773.5,-300.5 978.5,-300.5 978.5,-264.5 773.5,-264.5"/>
+<text text-anchor="middle" x="876" y="-277.45" font-family="Times,serif" font-size="14.00">isaSampleToRawDataSeq_arcPath</text>
+</g>
+<!-- isaSampleToRawDataSeq_arcPath->isaSampleToRawDataSeq -->
+<g id="edge3" class="edge">
+<title>isaSampleToRawDataSeq_arcPath->isaSampleToRawDataSeq</title>
+<path fill="none" stroke="black" d="M841.94,-264C820.12,-253.37 790.95,-240.22 764,-231.5 753.73,-228.18 742.83,-225.18 731.94,-222.51"/>
+<polygon fill="black" stroke="black" points="733.08,-219.18 722.55,-220.3 731.48,-226 733.08,-219.18"/>
+</g>
+<!-- isaSampleToRawDataSeq_assayName -->
+<g id="node5" class="node">
+<title>isaSampleToRawDataSeq_assayName</title>
+<polygon fill="#94ddf4" stroke="black" points="528.62,-264.5 528.62,-300.5 755.38,-300.5 755.38,-264.5 528.62,-264.5"/>
+<text text-anchor="middle" x="642" y="-277.45" font-family="Times,serif" font-size="14.00">isaSampleToRawDataSeq_assayName</text>
+</g>
+<!-- isaSampleToRawDataSeq_assayName->isaSampleToRawDataSeq -->
+<g id="edge4" class="edge">
+<title>isaSampleToRawDataSeq_assayName->isaSampleToRawDataSeq</title>
+<path fill="none" stroke="black" d="M642,-264.37C642,-255.55 642,-244.57 642,-234.51"/>
+<polygon fill="black" stroke="black" points="645.5,-234.84 642,-224.84 638.5,-234.84 645.5,-234.84"/>
+</g>
+<!-- isaSampleToRawDataSeq_outName -->
+<g id="node6" class="node">
+<title>isaSampleToRawDataSeq_outName</title>
+<polygon fill="#94ddf4" stroke="black" points="295.62,-264.5 295.62,-300.5 510.38,-300.5 510.38,-264.5 295.62,-264.5"/>
+<text text-anchor="middle" x="403" y="-277.45" font-family="Times,serif" font-size="14.00">isaSampleToRawDataSeq_outName</text>
+</g>
+<!-- isaSampleToRawDataSeq_outName->isaSampleToRawDataSeq -->
+<g id="edge5" class="edge">
+<title>isaSampleToRawDataSeq_outName->isaSampleToRawDataSeq</title>
+<path fill="none" stroke="black" d="M438.67,-264.07C461.49,-253.47 491.98,-240.32 520,-231.5 530.11,-228.32 540.82,-225.42 551.53,-222.81"/>
+<polygon fill="black" stroke="black" points="552.25,-226.24 561.18,-220.55 550.65,-219.42 552.25,-226.24"/>
+</g>
+<!-- isaSampleToRawDataSeq_startingNodeNum -->
+<g id="node7" class="node">
+<title>isaSampleToRawDataSeq_startingNodeNum</title>
+<polygon fill="#94ddf4" stroke="black" points="16,-264.5 16,-300.5 278,-300.5 278,-264.5 16,-264.5"/>
+<text text-anchor="middle" x="147" y="-277.45" font-family="Times,serif" font-size="14.00">isaSampleToRawDataSeq_startingNodeNum</text>
+</g>
+<!-- isaSampleToRawDataSeq_startingNodeNum->isaSampleToRawDataSeq -->
+<g id="edge6" class="edge">
+<title>isaSampleToRawDataSeq_startingNodeNum->isaSampleToRawDataSeq</title>
+<path fill="none" stroke="black" d="M186.6,-264.1C214.19,-252.79 252.15,-238.83 287,-231.5 375.68,-212.84 479.26,-207.19 551.56,-205.77"/>
+<polygon fill="black" stroke="black" points="551.44,-209.27 561.38,-205.6 551.32,-202.27 551.44,-209.27"/>
+</g>
+<!-- kallisto_BootstrapSamples -->
+<g id="node8" class="node">
+<title>kallisto_BootstrapSamples</title>
+<polygon fill="#94ddf4" stroke="black" points="1307.25,-264.5 1307.25,-300.5 1468.75,-300.5 1468.75,-264.5 1307.25,-264.5"/>
+<text text-anchor="middle" x="1388" y="-277.45" font-family="Times,serif" font-size="14.00">kallisto_BootstrapSamples</text>
+</g>
+<!-- kallisto_BootstrapSamples->kallisto -->
+<g id="edge7" class="edge">
+<title>kallisto_BootstrapSamples->kallisto</title>
+<path fill="none" stroke="black" d="M1413.65,-264.1C1431.07,-253.09 1455.04,-239.48 1478,-231.5 1516.32,-218.18 1562.41,-211.74 1594.51,-208.68"/>
+<polygon fill="black" stroke="black" points="1594.51,-212.19 1604.16,-207.83 1593.89,-205.22 1594.51,-212.19"/>
+</g>
+<!-- kallisto_FragmentLength -->
+<g id="node9" class="node">
+<title>kallisto_FragmentLength</title>
+<polygon fill="#94ddf4" stroke="black" points="1136.38,-264.5 1136.38,-300.5 1289.62,-300.5 1289.62,-264.5 1136.38,-264.5"/>
+<text text-anchor="middle" x="1213" y="-277.45" font-family="Times,serif" font-size="14.00">kallisto_FragmentLength</text>
+</g>
+<!-- kallisto_FragmentLength->kallisto -->
+<g id="edge8" class="edge">
+<title>kallisto_FragmentLength->kallisto</title>
+<path fill="none" stroke="black" d="M1235.81,-264.17C1252.18,-252.75 1275.29,-238.62 1298,-231.5 1352.25,-214.5 1517.79,-208.61 1594.37,-206.77"/>
+<polygon fill="black" stroke="black" points="1594.43,-210.27 1604.35,-206.54 1594.27,-203.27 1594.43,-210.27"/>
+</g>
+<!-- kallisto_IndexInput -->
+<g id="node10" class="node">
+<title>kallisto_IndexInput</title>
+<polygon fill="#94ddf4" stroke="black" points="996.12,-264.5 996.12,-300.5 1117.88,-300.5 1117.88,-264.5 996.12,-264.5"/>
+<text text-anchor="middle" x="1057" y="-277.45" font-family="Times,serif" font-size="14.00">kallisto_IndexInput</text>
+</g>
+<!-- kallisto_IndexInput->kallisto -->
+<g id="edge9" class="edge">
+<title>kallisto_IndexInput->kallisto</title>
+<path fill="none" stroke="black" d="M1074.93,-264.24C1088.17,-252.69 1107.26,-238.38 1127,-231.5 1170.61,-216.31 1482.71,-208.9 1594.39,-206.71"/>
+<polygon fill="black" stroke="black" points="1594.33,-210.21 1604.26,-206.52 1594.2,-203.21 1594.33,-210.21"/>
+</g>
+<!-- kallisto_StandardDeviation -->
+<g id="node11" class="node">
+<title>kallisto_StandardDeviation</title>
+<polygon fill="#94ddf4" stroke="black" points="1921.12,-264.5 1921.12,-300.5 2084.88,-300.5 2084.88,-264.5 1921.12,-264.5"/>
+<text text-anchor="middle" x="2003" y="-277.45" font-family="Times,serif" font-size="14.00">kallisto_StandardDeviation</text>
+</g>
+<!-- kallisto_StandardDeviation->kallisto -->
+<g id="edge10" class="edge">
+<title>kallisto_StandardDeviation->kallisto</title>
+<path fill="none" stroke="black" d="M1977.98,-264.06C1960.37,-252.74 1935.79,-238.78 1912,-231.5 1868.5,-218.19 1739.3,-210.69 1673.49,-207.63"/>
+<polygon fill="black" stroke="black" points="1674.01,-204.15 1663.86,-207.2 1673.69,-211.15 1674.01,-204.15"/>
+</g>
+<!-- kallisto_isSingle -->
+<g id="node12" class="node">
+<title>kallisto_isSingle</title>
+<polygon fill="#94ddf4" stroke="black" points="1797,-264.5 1797,-300.5 1903,-300.5 1903,-264.5 1797,-264.5"/>
+<text text-anchor="middle" x="1850" y="-277.45" font-family="Times,serif" font-size="14.00">kallisto_isSingle</text>
+</g>
+<!-- kallisto_isSingle->kallisto -->
+<g id="edge11" class="edge">
+<title>kallisto_isSingle->kallisto</title>
+<path fill="none" stroke="black" d="M1833.47,-264.16C1821.83,-253.02 1805.29,-239.25 1788,-231.5 1751.33,-215.06 1705.47,-209.11 1673.37,-207.01"/>
+<polygon fill="black" stroke="black" points="1673.9,-203.54 1663.72,-206.49 1673.51,-210.53 1673.9,-203.54"/>
+</g>
+<!-- kallisto_resultsFolder -->
+<g id="node13" class="node">
+<title>kallisto_resultsFolder</title>
+<polygon fill="#94ddf4" stroke="black" points="1645.5,-264.5 1645.5,-300.5 1778.5,-300.5 1778.5,-264.5 1645.5,-264.5"/>
+<text text-anchor="middle" x="1712" y="-277.45" font-family="Times,serif" font-size="14.00">kallisto_resultsFolder</text>
+</g>
+<!-- kallisto_resultsFolder->kallisto -->
+<g id="edge12" class="edge">
+<title>kallisto_resultsFolder->kallisto</title>
+<path fill="none" stroke="black" d="M1694.3,-264.37C1684.2,-254.59 1671.35,-242.15 1660.11,-231.27"/>
+<polygon fill="black" stroke="black" points="1662.61,-228.82 1652.99,-224.38 1657.74,-233.85 1662.61,-228.82"/>
+</g>
+<!-- kallisto_sampleRecord -->
+<g id="node14" class="node">
+<title>kallisto_sampleRecord</title>
+<polygon fill="#94ddf4" stroke="black" points="1486.75,-264.5 1486.75,-300.5 1627.25,-300.5 1627.25,-264.5 1486.75,-264.5"/>
+<text text-anchor="middle" x="1557" y="-277.45" font-family="Times,serif" font-size="14.00">kallisto_sampleRecord</text>
+</g>
+<!-- kallisto_sampleRecord->kallisto -->
+<g id="edge13" class="edge">
+<title>kallisto_sampleRecord->kallisto</title>
+<path fill="none" stroke="black" d="M1574.47,-264.37C1584.44,-254.59 1597.13,-242.15 1608.23,-231.27"/>
+<polygon fill="black" stroke="black" points="1610.56,-233.89 1615.25,-224.39 1605.66,-228.89 1610.56,-233.89"/>
+</g>
+<!-- sleuth_inMetadataDataCol -->
+<g id="node15" class="node">
+<title>sleuth_inMetadataDataCol</title>
+<polygon fill="#94ddf4" stroke="black" points="2103.25,-264.5 2103.25,-300.5 2264.75,-300.5 2264.75,-264.5 2103.25,-264.5"/>
+<text text-anchor="middle" x="2184" y="-277.45" font-family="Times,serif" font-size="14.00">sleuth_inMetadataDataCol</text>
+</g>
+<!-- sleuth_inMetadataDataCol->sleuth -->
+<g id="edge14" class="edge">
+<title>sleuth_inMetadataDataCol->sleuth</title>
+<path fill="none" stroke="black" d="M2194.73,-264.17C2210.66,-238.47 2240.68,-190 2259.44,-159.73"/>
+<polygon fill="black" stroke="black" points="2262.25,-161.85 2264.54,-151.5 2256.3,-158.16 2262.25,-161.85"/>
+</g>
+<!-- sleuth_inMetadataFactorList -->
+<g id="node16" class="node">
+<title>sleuth_inMetadataFactorList</title>
+<polygon fill="#94ddf4" stroke="black" points="2283,-264.5 2283,-300.5 2455,-300.5 2455,-264.5 2283,-264.5"/>
+<text text-anchor="middle" x="2369" y="-277.45" font-family="Times,serif" font-size="14.00">sleuth_inMetadataFactorList</text>
+</g>
+<!-- sleuth_inMetadataFactorList->sleuth -->
+<g id="edge15" class="edge">
+<title>sleuth_inMetadataFactorList->sleuth</title>
+<path fill="none" stroke="black" d="M2358.15,-264.17C2342.05,-238.47 2311.7,-190 2292.74,-159.73"/>
+<polygon fill="black" stroke="black" points="2295.86,-158.12 2287.58,-151.5 2289.93,-161.83 2295.86,-158.12"/>
+</g>
+<!-- sleuth_inMetadataSample -->
+<g id="node17" class="node">
+<title>sleuth_inMetadataSample</title>
+<polygon fill="#94ddf4" stroke="black" points="2473.12,-264.5 2473.12,-300.5 2630.88,-300.5 2630.88,-264.5 2473.12,-264.5"/>
+<text text-anchor="middle" x="2552" y="-277.45" font-family="Times,serif" font-size="14.00">sleuth_inMetadataSample</text>
+</g>
+<!-- sleuth_inMetadataSample->sleuth -->
+<g id="edge16" class="edge">
+<title>sleuth_inMetadataSample->sleuth</title>
+<path fill="none" stroke="black" d="M2522,-264.12C2505.06,-254.39 2483.43,-242.11 2464,-231.5 2412.12,-203.18 2351.44,-171.67 2313.35,-152.1"/>
+<polygon fill="black" stroke="black" points="2315.08,-149.05 2304.59,-147.59 2311.88,-155.28 2315.08,-149.05"/>
+</g>
+<!-- sleuth_outFolder -->
+<g id="node18" class="node">
+<title>sleuth_outFolder</title>
+<polygon fill="#94ddf4" stroke="black" points="2649.25,-264.5 2649.25,-300.5 2756.75,-300.5 2756.75,-264.5 2649.25,-264.5"/>
+<text text-anchor="middle" x="2703" y="-277.45" font-family="Times,serif" font-size="14.00">sleuth_outFolder</text>
+</g>
+<!-- sleuth_outFolder->sleuth -->
+<g id="edge17" class="edge">
+<title>sleuth_outFolder->sleuth</title>
+<path fill="none" stroke="black" d="M2685.09,-264C2673.18,-253.24 2656.7,-239.93 2640,-231.5 2529.23,-175.57 2382.96,-148.47 2314.47,-138.16"/>
+<polygon fill="black" stroke="black" points="2315.28,-134.74 2304.88,-136.76 2314.27,-141.67 2315.28,-134.74"/>
+</g>
+</g>
+</svg>
diff --git a/arc.cwl b/arc.cwl
index e0a4ce9..82171c7 100644
--- a/arc.cwl
+++ b/arc.cwl
@@ -70,11 +70,11 @@ steps:
inMetadataSample: sleuth_inMetadataSample
inMetadataFactorList: sleuth_inMetadataFactorList
inMetadataDataCol: sleuth_inMetadataDataCol
- outFolder: sleuth_outFolder
+ resultsoutdir: sleuth_outFolder
out: [outdir]
outputs:
outdir:
- type: Directory[]
+ type: Directory
outputSource: sleuth/outdir
\ No newline at end of file
--
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