diff --git a/.cwl/README.md b/.cwl/README.md
index 41a62d0781782aa6192559d788c3dbcc500c32fe..0340cecc65fb7ceb4db7bbef0e16242b04eac63d 100644
--- a/.cwl/README.md
+++ b/.cwl/README.md
@@ -77,5 +77,5 @@ cwltool --parallel run.cwl run.yml > $(date +"%Y-%m-%d_%H-%M")-run.log 2>&1 &
### Print workflow to file
```bash
-cwltool --print-dot run.cwl | dot -Tsvg > run.svg
+cwltool --print-dot ../arc.cwl | dot -Tsvg > arc-cwl.svg
```
diff --git a/.cwl/arc-cwl.svg b/.cwl/arc-cwl.svg
new file mode 100644
index 0000000000000000000000000000000000000000..8269aa869ea0ca21187fc6241694f3b86598ec00
--- /dev/null
+++ b/.cwl/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/.cwl/cwl-plots/runs/kallisto.svg b/.cwl/cwl-plots/runs/kallisto.svg
index 45f69bc844193654382928997d43f78b3e2171f4..241535b57ea69b5af61d7e5f40ede4a8366fdb7f 100644
--- a/.cwl/cwl-plots/runs/kallisto.svg
+++ b/.cwl/cwl-plots/runs/kallisto.svg
@@ -109,15 +109,15 @@
<path fill="none" stroke="black" d="M79.18,-185.43C89.76,-174.74 104.84,-161.76 121,-155 157.69,-139.66 267.22,-133.56 330.49,-131.27"/>
<polygon fill="black" stroke="black" points="330.73,-134.77 340.61,-130.93 330.49,-127.77 330.73,-134.77"/>
</g>
-<!-- finalOut -->
+<!-- kallistoOutDir -->
<g id="node9" class="node">
-<title>finalOut</title>
+<title>kallistoOutDir</title>
<polygon fill="#94ddf4" stroke="black" points="346.06,-38.5 346.06,-74.5 407.94,-74.5 407.94,-38.5 346.06,-38.5"/>
-<text text-anchor="middle" x="377" y="-52.3" font-family="Times,serif" font-size="14.00">finalOut</text>
+<text text-anchor="middle" x="377" y="-52.3" font-family="Times,serif" font-size="14.00">kallistoOutDir</text>
</g>
-<!-- kallisto->finalOut -->
+<!-- kallisto->kallistoOutDir -->
<g id="edge8" class="edge">
-<title>kallisto->finalOut</title>
+<title>kallisto->kallistoOutDir</title>
<path fill="none" stroke="black" d="M377,-110.93C377,-103.17 377,-93.78 377,-85.06"/>
<polygon fill="black" stroke="black" points="380.5,-84.9 377,-74.9 373.5,-84.9 380.5,-84.9"/>
</g>
diff --git a/.cwl/cwl-plots/workflows/kallisto.svg b/.cwl/cwl-plots/workflows/kallisto.svg
index 9e81b888aae33970cf281e5cb9f209c6c363d61a..930b4cad82f95e6624a32284127342621d8e2618 100644
--- a/.cwl/cwl-plots/workflows/kallisto.svg
+++ b/.cwl/cwl-plots/workflows/kallisto.svg
@@ -37,15 +37,15 @@
<path fill="none" stroke="black" d="M491.95,-193.08C456.78,-182.13 394.44,-162.71 348.49,-148.4"/>
<polygon fill="black" stroke="black" points="349.25,-144.97 338.66,-145.34 347.16,-151.66 349.25,-144.97"/>
</g>
-<!-- finalOut -->
+<!-- kallistoOutDir -->
<g id="node11" class="node">
-<title>finalOut</title>
+<title>kallistoOutDir</title>
<polygon fill="#94ddf4" stroke="black" points="260.06,-38.5 260.06,-74.5 321.94,-74.5 321.94,-38.5 260.06,-38.5"/>
-<text text-anchor="middle" x="291" y="-52.3" font-family="Times,serif" font-size="14.00">finalOut</text>
+<text text-anchor="middle" x="291" y="-52.3" font-family="Times,serif" font-size="14.00">kallistoOutDir</text>
</g>
-<!-- collectResults->finalOut -->
+<!-- collectResults->kallistoOutDir -->
<g id="edge12" class="edge">
-<title>collectResults->finalOut</title>
+<title>collectResults->kallistoOutDir</title>
<path fill="none" stroke="black" d="M291,-111.31C291,-103.29 291,-93.55 291,-84.57"/>
<polygon fill="black" stroke="black" points="294.5,-84.53 291,-74.53 287.5,-84.53 294.5,-84.53"/>
</g>
diff --git a/README.md b/README.md
index a0b47600f691b2402d98bfee41e34da7a0c1b704..ffc8756d26c797bc40c8fc58d9465445cea5c79e 100644
--- a/README.md
+++ b/README.md
@@ -5,15 +5,29 @@ The [Talinum Genome Draft](./studies/TalinumGenomeDraft) originates from <https:
## Table of Contents
-1. [Description](#description)
-2. [Publication](#publication)
-3. Studies
- - [TalinumGenomeDraft](#study--talinumgenomedraft)
- - [TalinumSamples-STRI](#study--TalinumSamples-STRI)
-4. Assays
- - [MassHunter_targets](#assay--masshunter_targets)
- - [GCqTOF_targets](#assay--gcqtof_targets)
- - [RNASeq](#assay--RNASeq)
+- [Table of Contents](#table-of-contents)
+ - [Description](#description)
+- [Relationships between Assays and Studies](#relationships-between-assays-and-studies)
+- [Workflow Overview](#workflow-overview)
+- [Additional details](#additional-details)
+- [Publication](#publication)
+- [Study : *TalinumGenomeDraft*](#study--talinumgenomedraft)
+ - [Additional details](#additional-details-1)
+ - [Annotation headers](#annotation-headers)
+- [Study : *TalinumSamples-STRI*](#study--talinumsamples-stri)
+ - [Additional details](#additional-details-2)
+ - [Annotation headers](#annotation-headers-1)
+- [Assay : *MassHunter\_targets*](#assay--masshunter_targets)
+ - [Additional details](#additional-details-3)
+ - [Annotation headers](#annotation-headers-2)
+- [Assay : *RNASeq*](#assay--rnaseq)
+ - [Additional details](#additional-details-4)
+ - [Annotation headers](#annotation-headers-3)
+- [Assay : *GCqTOF\_targets*](#assay--gcqtof_targets)
+ - [Additional details](#additional-details-5)
+ - [Annotation headers](#annotation-headers-4)
+
+
### Description
@@ -67,7 +81,12 @@ class ASSAY_MassHunter_targets,ASSAY_RNASeq,ASSAY_GCqTOF_targets assayStyle;
class TalinumGenomeDraft,plant_material,mh-quant-results,mh-quant-report,rna_extraction,illumina,metabolite_extraction,gas_chromatography,mass_spec processStyle;
```
-### Additional details
+## Workflow Overview
+
+
+
+
+## Additional details
| Meta Data | Description |
| --------- | ----------- |
diff --git a/arc-job.yml b/arc-job.yml
new file mode 100644
index 0000000000000000000000000000000000000000..9b36300bc49b2cf45ad8b50d87cfd2cad1c8de22
--- /dev/null
+++ b/arc-job.yml
@@ -0,0 +1,76 @@
+################################################################################
+### runs/kallisto
+################################################################################
+
+## Genome file to build kallisto Index
+kallisto_IndexInput:
+ - class: File
+ path: ./studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
+ format: edam:format_1929 # FASTA
+
+## Fastq files to be mapped
+# The `readsOfOneSample` looks more complicated than needed
+# It's an array of records (each with one or mupltiple files and a sample name) to generically allow multiple fastq files per sample
+
+kallisto_sampleRecord:
+ - readsOfOneSample:
+ - class: File
+ path: ./assays/RNASeq/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
+ format: edam:format_1930
+ sampleName: 'DB_097'
+ - readsOfOneSample:
+ - class: File
+ path: ./assays/RNASeq/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
+ format: edam:format_1930
+ sampleName: 'DB_163'
+ - readsOfOneSample:
+ - class: File
+ path: ./assays/RNASeq/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
+ format: edam:format_1930
+ sampleName: 'DB_099'
+ - readsOfOneSample:
+ - class: File
+ path: ./assays/RNASeq/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
+ format: edam:format_1930
+ sampleName: 'DB_103'
+ - readsOfOneSample:
+ - class: File
+ path: ./assays/RNASeq/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
+ format: edam:format_1930
+ sampleName: 'DB_161'
+ - readsOfOneSample:
+ - class: File
+ path: ./assays/RNASeq/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
+ format: edam:format_1930
+ sampleName: 'DB_165'
+
+### Kallisto quant Parameters
+kallisto_isSingle: true
+kallisto_FragmentLength: 200
+kallisto_StandardDeviation: 20
+kallisto_BootstrapSamples: 30
+kallisto_resultsFolder: kallisto_results
+
+$namespaces:
+ edam: https://edamontology.org/
+
+################################################################################
+### runs/isaSampleToRawDataSeq
+################################################################################
+
+isaSampleToRawDataSeq_arcPath:
+ class: Directory
+ path: ./
+isaSampleToRawDataSeq_assayName: "RNASeq"
+isaSampleToRawDataSeq_outName: rnaseq-samples
+isaSampleToRawDataSeq_startingNodeNum: 0
+
+################################################################################
+### runs/sleuth
+################################################################################
+
+sleuth_inMetadataSample: "Input [Source Name]"
+sleuth_inMetadataFactorList:
+ - "Factor [Photosynthesis mode]"
+sleuth_inMetadataDataCol: "Output [Data]"
+sleuth_outFolder: results
diff --git a/arc.cwl b/arc.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..e0a4ce99f8aec508b687d0eeeb0822d7e04c943a
--- /dev/null
+++ b/arc.cwl
@@ -0,0 +1,80 @@
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+ SubworkflowFeatureRequirement: {}
+ ScatterFeatureRequirement: {}
+ MultipleInputFeatureRequirement: {}
+
+inputs:
+ #### runs/kallisto
+ kallisto_IndexInput: File[]
+ kallisto_sampleRecord:
+ type:
+ type: array
+ items:
+ type: record
+ fields:
+ readsOfOneSample:
+ type: File[]
+ sampleName:
+ type: string?
+ kallisto_isSingle: boolean
+ kallisto_FragmentLength: double?
+ kallisto_StandardDeviation: double?
+ kallisto_BootstrapSamples: int?
+ kallisto_resultsFolder: string
+
+ #### runs/isaSampleToRawDataSeq
+ isaSampleToRawDataSeq_arcPath: Directory
+ isaSampleToRawDataSeq_assayName: string
+ isaSampleToRawDataSeq_startingNodeNum: int
+ isaSampleToRawDataSeq_outName: string
+
+ #### runs/sleuth
+# sleuth_inKallistoResults: Directory
+# sleuth_inMetadataFile: File
+ sleuth_inMetadataSample: string
+ sleuth_inMetadataFactorList: string[]
+ sleuth_inMetadataDataCol: string
+ sleuth_outFolder: string
+
+steps:
+ kallisto:
+ run: runs/kallisto/run.cwl
+ in:
+ IndexInput: kallisto_IndexInput
+ sampleRecord: kallisto_sampleRecord
+ isSingle: kallisto_isSingle
+ FragmentLength: kallisto_FragmentLength
+ StandardDeviation: kallisto_StandardDeviation
+ BootstrapSamples: kallisto_BootstrapSamples
+ resultsFolder: kallisto_resultsFolder
+ out: [kallistoOutDir]
+
+
+ isaSampleToRawDataSeq:
+ run: runs/isaSampleToRawDataSeq/run.cwl
+ in:
+ arcPath: isaSampleToRawDataSeq_arcPath
+ assayName: isaSampleToRawDataSeq_assayName
+ startingNodeNum: isaSampleToRawDataSeq_startingNodeNum
+ outName: isaSampleToRawDataSeq_outName
+ out: [sampleseqCsv, sampleseqXlsx]
+
+ sleuth:
+ run: runs/sleuth/run.cwl
+ in:
+ inKallistoResults: kallisto/kallistoOutDir
+ inMetadataFile: isaSampleToRawDataSeq/sampleseqCsv
+ inMetadataSample: sleuth_inMetadataSample
+ inMetadataFactorList: sleuth_inMetadataFactorList
+ inMetadataDataCol: sleuth_inMetadataDataCol
+ outFolder: sleuth_outFolder
+ out: [outdir]
+
+outputs:
+
+ outdir:
+ type: Directory[]
+ outputSource: sleuth/outdir
\ No newline at end of file
diff --git a/runs/fastqc/run.cwl b/runs/fastqc/run.cwl
index 974e99274b8fab4201a548c27fdda57f059544b4..b049a5f92ccca308657a8791af4c5d52f3871da3 100644
--- a/runs/fastqc/run.cwl
+++ b/runs/fastqc/run.cwl
@@ -16,9 +16,9 @@ steps:
in:
fastq: fastq
finaloutdir: finaloutdir
- out: [outdir]
+ out: [fastqc_outdir]
outputs:
- outdir:
+ fastqc_outdir:
type: Directory
- outputSource: fastqc/outdir
\ No newline at end of file
+ outputSource: fastqc/fastqc_outdir
\ No newline at end of file
diff --git a/runs/isaSampleToRawDataSeq/rnaseq-samples.xlsx b/runs/isaSampleToRawDataSeq/rnaseq-samples.xlsx
index 1c05d363efc105474dc4887ac57f94beba0ac181..e73d722501815a8b129f9f7a95b3b0af60c45ab0 100644
Binary files a/runs/isaSampleToRawDataSeq/rnaseq-samples.xlsx and b/runs/isaSampleToRawDataSeq/rnaseq-samples.xlsx differ
diff --git a/runs/isaSampleToRawDataSeq/run.cwl b/runs/isaSampleToRawDataSeq/run.cwl
index 8f00f6abfd1d3f757b20fdf253fbbcd0b0003aa5..aca29e7543721a02e4a3a7eee0650b1167615a0f 100644
--- a/runs/isaSampleToRawDataSeq/run.cwl
+++ b/runs/isaSampleToRawDataSeq/run.cwl
@@ -15,10 +15,14 @@ steps:
assayName: assayName
startingNodeNum: startingNodeNum
outName: outName
- out: [output]
+ out:
+ - sampleseqCsv
+ - sampleseqXlsx
outputs:
- output:
- type: File[]
- outputSource: isaSampleToRawDataSeq/output
-
+ sampleseqCsv:
+ type: File
+ outputSource: isaSampleToRawDataSeq/sampleseqCsv
+ sampleseqXlsx:
+ type: File
+ outputSource: isaSampleToRawDataSeq/sampleseqXlsx
\ No newline at end of file
diff --git a/runs/kallisto/run.cwl b/runs/kallisto/run.cwl
index 3ec2a22fd3d933361182dff470de94caf611a092..d702ed4426bff5a1890b4f9f0ce0de6acb1743c8 100644
--- a/runs/kallisto/run.cwl
+++ b/runs/kallisto/run.cwl
@@ -35,9 +35,9 @@ steps:
StandardDeviation: StandardDeviation
BootstrapSamples: BootstrapSamples
resultsFolder: resultsFolder
- out: [finalOut]
+ out: [kallistoOutDir]
outputs:
- finalOut:
- type: Directory[]
- outputSource: kallisto/finalOut
+ kallistoOutDir:
+ type: Directory
+ outputSource: kallisto/kallistoOutDir
diff --git a/runs/sleuth/run.cwl b/runs/sleuth/run.cwl
index b21434225a867157c64962fcf079f36b19d302b5..e00ce51a124f5266ae6f383ba5d21ba4383ffc57 100644
--- a/runs/sleuth/run.cwl
+++ b/runs/sleuth/run.cwl
@@ -12,7 +12,7 @@ inputs:
outFolder: string
steps:
- collectResults:
+ sleuth:
run: ../../workflows/sleuth/workflow.cwl
in:
inKallistoResults: inKallistoResults
@@ -26,4 +26,4 @@ steps:
outputs:
outdir:
type: Directory[]
- outputSource: collectResults/outdir
+ outputSource: sleuth/outdir
diff --git a/workflows/fastqc/collectFilesInDir.cwl b/workflows/fastqc/collectFilesInDir.cwl
deleted file mode 100644
index 39f9ff8ae5a33d939136c081a9cd79533972eddc..0000000000000000000000000000000000000000
--- a/workflows/fastqc/collectFilesInDir.cwl
+++ /dev/null
@@ -1,20 +0,0 @@
-cwlVersion: v1.2
-class: ExpressionTool
-label: Collect files in a directory
-doc: |
- Takes Files (e.g. from a workflow step) and yields them in a desired directory.
-requirements:
- - class: InlineJavascriptRequirement
-inputs:
- files: File[]
- destination: string
-expression: |
- ${
- return {"outDir": {
- "class": "Directory",
- "basename": inputs.destination,
- "listing": inputs.files
- } };
- }
-outputs:
- outDir: Directory
\ No newline at end of file
diff --git a/workflows/fastqc/fastqc.cwl b/workflows/fastqc/fastqc.cwl
index a2e408db732fa6913af001c6349dda4ac30a116e..f0b906a85f919f4547565b27a3254ad4404c8824 100644
--- a/workflows/fastqc/fastqc.cwl
+++ b/workflows/fastqc/fastqc.cwl
@@ -2,12 +2,14 @@
cwlVersion: v1.2
class: CommandLineTool
-label: Run fastqc on raw reads in FASTQ format (single or paired end) or aligned reads in BAM.
+label: FastQC - A high throughput sequence QC analysis tool
doc: |
- simplified from: https://github.com/common-workflow-library/bio-cwl-tools/blob/66f620da5b0a11e934a6da83272205a2516bcd91/fastqc/fastqc_1.cwl
-
+ Original docs: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+
Run fastqc on raw reads in FASTQ format (single or paired end) or aligned reads in BAM.
+
+ This CWL was adapted from: https://github.com/common-workflow-library/bio-cwl-tools/blob/66f620da5b0a11e934a6da83272205a2516bcd91/fastqc/fastqc_1.cwl
hints:
ResourceRequirement:
@@ -18,11 +20,13 @@ hints:
SoftwareRequirement:
packages:
fastqc:
- specs: [ https://identifiers.org/biotools/fastqc ]
+ specs:
+ - https://identifiers.org/biotools/fastqc
+ - - https://identifiers.org/rrid/RRID:SCR_014583
version: [ "0.11.9" ]
-
baseCommand: "fastqc"
+
arguments:
- valueFrom: $(runtime.outdir)
prefix: "-o"
@@ -46,3 +50,13 @@ outputs:
outputBinding:
glob: "*_fastqc.html"
+
+$namespaces:
+ edam: https://edamontology.org/
+ s: https://schema.org/
+$schemas:
+ - https://edamontology.org/EDAM_1.18.owl
+
+s:license: https://spdx.org/licenses/GPL-3.0-or-later
+
+
diff --git a/workflows/fastqc/gather-files.cwl b/workflows/fastqc/gather-files.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..67d23ec72e90012c4e07b2f2ebaf3b2d102308c8
--- /dev/null
+++ b/workflows/fastqc/gather-files.cwl
@@ -0,0 +1,24 @@
+cwlVersion: v1.2
+class: ExpressionTool
+label: Gather files
+doc: |
+ Helper tool to organize workflow outputs
+
+ Takes an array of files (e.g. from a workflow step) and yields them in a destination directory.
+
+ Adapted from: https://github.com/common-workflow-language/cwl-v1.1/blob/a22b7580c6b50e77c0a181ca59d3828dd5c69143/tests/dir7.cwl
+requirements:
+ - class: InlineJavascriptRequirement
+inputs:
+ inFiles: File[]
+ destination: string
+expression: |
+ ${
+ return {"outDir": {
+ "class": "Directory",
+ "basename": inputs.destination,
+ "listing": inputs.inFiles
+ } };
+ }
+outputs:
+ outDir: Directory
\ No newline at end of file
diff --git a/workflows/fastqc/workflow.cwl b/workflows/fastqc/workflow.cwl
index d80a7eaafc7c6f530d3c43ca21716b005e7d1f4e..45923196e84b10785fbf079d4fe4c2d8397abfa4 100644
--- a/workflows/fastqc/workflow.cwl
+++ b/workflows/fastqc/workflow.cwl
@@ -18,15 +18,17 @@ steps:
fastq: fastq
out: [fastqc_zip, fastqc_html]
collectFiles:
- run: ./collectFilesInDir.cwl
+ run: ./gather-files.cwl
in:
- destination: finaloutdir
- files:
- source: [fastqc/fastqc_html, fastqc/fastqc_zip]
+ inFiles:
+ source:
+ - fastqc/fastqc_html
+ - fastqc/fastqc_zip
linkMerge: merge_flattened
+ destination: finaloutdir
out: [outDir]
outputs:
- outdir:
+ fastqc_outdir:
type: Directory
outputSource: collectFiles/outDir
\ No newline at end of file
diff --git a/workflows/isaSampleToRawDataSeq/workflow.cwl b/workflows/isaSampleToRawDataSeq/workflow.cwl
index 9cace450b08381d8a8dc408daf6fab25489e8881..f9db3ee3cc8a9dcd6cb12b963d0728cdbb247c70 100644
--- a/workflows/isaSampleToRawDataSeq/workflow.cwl
+++ b/workflows/isaSampleToRawDataSeq/workflow.cwl
@@ -39,9 +39,13 @@ inputs:
position: 4
outputs:
- output:
- type: File[]
+ sampleseqCsv:
+ type: File
outputBinding:
glob:
- "*.csv"
+ sampleseqXlsx:
+ type: File
+ outputBinding:
+ glob:
- "*.xlsx"
diff --git a/workflows/kallisto/gather-dirs.cwl b/workflows/kallisto/gather-dirs.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..858682309d3ce7fef50d7d71741832f9ecdde0ae
--- /dev/null
+++ b/workflows/kallisto/gather-dirs.cwl
@@ -0,0 +1,28 @@
+cwlVersion: v1.2
+class: ExpressionTool
+label: Gather directories
+doc: |
+ Helper tool to organize workflow outputs
+
+ Takes an array of directories (e.g. from a workflow step) and yields them in a destination directory.
+
+ Adapted from: https://github.com/common-workflow-language/cwl-v1.1/blob/a22b7580c6b50e77c0a181ca59d3828dd5c69143/tests/dir7.cwl
+
+requirements:
+ - class: InlineJavascriptRequirement
+
+inputs:
+ inDirs: Directory[]
+ destinationDir: string
+
+expression: |
+ ${
+ return {"outDir": {
+ "class": "Directory",
+ "basename": inputs.destinationDir,
+ "listing": inputs.inDirs
+ } };
+ }
+
+outputs:
+ outDir: Directory
\ No newline at end of file
diff --git a/workflows/kallisto/kallisto-index.cwl b/workflows/kallisto/kallisto-index.cwl
index d35f52022fabbb4028a84fe2866fbf3343122947..b43cba7adfe32a26892de9acff2d747d20c4e28f 100644
--- a/workflows/kallisto/kallisto-index.cwl
+++ b/workflows/kallisto/kallisto-index.cwl
@@ -2,17 +2,47 @@
cwlVersion: v1.2
class: CommandLineTool
+label: Kallisto index
+doc: |
+
+ Docs: https://pachterlab.github.io/kallisto/
+
+
+ Builds a kallisto index
+
+ Usage: kallisto index [arguments] FASTA-files
+
+ Required argument:
+ -i, --index=STRING Filename for the kallisto index to be constructed
+
+ Optional argument:
+ -k, --kmer-size=INT k-mer (odd) length (default: 31, max value: 63)
+ -t, --threads=INT Number of threads to use (default: 1)
+ -d, --d-list=STRING Path to a FASTA-file containing sequences to mask from quantification
+ --make-unique Replace repeated target names with unique names
+ --aa Generate index from a FASTA-file containing amino acid sequences
+ --distinguish Generate index where sequences are distinguished by the sequence name
+ -T, --tmp=STRING Temporary directory (default: tmp)
+ -m, --min-size=INT Length of minimizers (default: automatically chosen)
+ -e, --ec-max-size=INT Maximum number of targets in an equivalence class (default: no maximum)
+
+ This CWL was adapted from: https://github.com/common-workflow-library/bio-cwl-tools/commit/91c42fb809ce18eafe16155cca0abf362270c0fe
+
hints:
DockerRequirement:
dockerPull: quay.io/biocontainers/kallisto:0.51.1--ha4fb952_1
SoftwareRequirement:
packages:
kallisto:
- version: [ "0.50.0" ]
- specs: [ https://identifiers.org/biotools/kallisto ]
+ version: [ "0.51.1" ]
+ specs:
+ - https://identifiers.org/rrid/RRID:SCR_016582
+ - https://identifiers.org/biotools/kallisto
requirements:
- - class: InlineJavascriptRequirement
+ InlineJavascriptRequirement: {}
+
+baseCommand: [kallisto, index]
inputs:
InputFiles:
@@ -41,8 +71,6 @@ inputs:
inputBinding:
prefix: "--make-unique"
-baseCommand: [kallisto, index]
-
outputs:
index:
type: File
@@ -51,5 +79,8 @@ outputs:
$namespaces:
edam: https://edamontology.org/
+ s: https://schema.org/
$schemas:
- https://edamontology.org/EDAM_1.18.owl
+
+s:license: https://spdx.org/licenses/BSD-2-Clause
diff --git a/workflows/kallisto/kallisto-quant.cwl b/workflows/kallisto/kallisto-quant.cwl
index 026f7e1bc37dba078b750b3f7ecb70019c4bc753..998c371f230cec6cabb4ea1f194b88510205fa0c 100755
--- a/workflows/kallisto/kallisto-quant.cwl
+++ b/workflows/kallisto/kallisto-quant.cwl
@@ -2,13 +2,51 @@
cwlVersion: v1.2
class: CommandLineTool
+label: Kallisto quant
+doc: |
+
+ Docs: https://pachterlab.github.io/kallisto/
+
+ Computes equivalence classes for reads and quantifies abundances
+
+ Usage: kallisto quant [arguments] FASTQ-files
+
+ Required arguments:
+ -i, --index=STRING Filename for the kallisto index to be used for
+ quantification
+ -o, --output-dir=STRING Directory to write output to
+
+ Optional arguments:
+ -b, --bootstrap-samples=INT Number of bootstrap samples (default: 0)
+ --seed=INT Seed for the bootstrap sampling (default: 42)
+ --plaintext Output plaintext instead of HDF5
+ --single Quantify single-end reads
+ --single-overhang Include reads where unobserved rest of fragment is
+ predicted to lie outside a transcript
+ --fr-stranded Strand specific reads, first read forward
+ --rf-stranded Strand specific reads, first read reverse
+ -l, --fragment-length=DOUBLE Estimated average fragment length
+ -s, --sd=DOUBLE Estimated standard deviation of fragment length
+ (default: -l, -s values are estimated from paired
+ end data, but are required when using --single)
+ -p, --priors Priors for the EM algorithm, either as raw counts or as
+ probabilities. Pseudocounts are added to raw reads to
+ prevent zero valued priors. Supplied in the same order
+ as the transcripts in the transcriptome
+ -t, --threads=INT Number of threads to use (default: 1)
+ --verbose Print out progress information every 1M proccessed reads
+
+
+ This CWL was adapted from: https://github.com/common-workflow-library/bio-cwl-tools/commit/91c42fb809ce18eafe16155cca0abf362270c0fe
+
+
hints:
DockerRequirement:
dockerPull: quay.io/biocontainers/kallisto:0.51.1--ha4fb952_1
SoftwareRequirement:
packages:
kallisto:
- version: [ "0.50.0" ]
+ version: [ "0.51.1" ]
specs: [ https://identifiers.org/biotools/kallisto ]
inputs:
@@ -126,12 +164,16 @@ arguments: [ "--output-dir", $(inputs.QuantOutfolder) ]
outputs:
- outFolder:
+ kallistoQuantOutDir:
type: Directory
outputBinding:
glob: $(runtime.outdir)/$(inputs.QuantOutfolder)
+
$namespaces:
edam: https://edamontology.org/
+ s: https://schema.org/
$schemas:
- https://edamontology.org/EDAM_1.18.owl
+
+s:license: https://spdx.org/licenses/BSD-2-Clause
diff --git a/workflows/kallisto/kallisto-test.cwl b/workflows/kallisto/kallisto-test.cwl
deleted file mode 100644
index 3a05871190f87a7d8436644c9db41b14fa73b758..0000000000000000000000000000000000000000
--- a/workflows/kallisto/kallisto-test.cwl
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env cwl-runner
-cwlVersion: v1.2
-class: CommandLineTool
-
-hints:
- DockerRequirement:
- dockerPull: quay.io/biocontainers/kallisto:0.50.1--h6de1650_2
- SoftwareRequirement:
- packages:
- kallisto:
- version: [ "0.50.0" ]
- specs: [ https://identifiers.org/biotools/kallisto ]
-
-inputs: []
-
-baseCommand: [kallisto]
-
-outputs: []
\ No newline at end of file
diff --git a/workflows/kallisto/workflow.cwl b/workflows/kallisto/workflow.cwl
index 4ce56173769787379dddf9cd977d60b18e6ff9c1..3120f96bc99f073fa144ccbe49fbf4fd7e52772e 100644
--- a/workflows/kallisto/workflow.cwl
+++ b/workflows/kallisto/workflow.cwl
@@ -8,60 +8,59 @@ requirements:
InlineJavascriptRequirement: {}
inputs:
- IndexInput: File[]
- sampleRecord:
- type:
- type: array
- items:
- type: record
- fields:
- readsOfOneSample:
- type: File[]
- sampleName:
- type: string?
- isSingle: boolean
- FragmentLength: double?
- StandardDeviation: double?
- BootstrapSamples: int?
- resultsFolder: string
+ IndexInput: File[]
+ sampleRecord:
+ type:
+ type: array
+ items:
+ type: record
+ fields:
+ readsOfOneSample:
+ type: File[]
+ sampleName:
+ type: string?
+ isSingle: boolean
+ FragmentLength: double?
+ StandardDeviation: double?
+ BootstrapSamples: int?
+ resultsFolder: string
steps:
- index:
- run: kallisto-index.cwl
- in:
- InputFiles: IndexInput
- IndexName:
- source: IndexInput
- valueFrom: $(self[0].nameroot)
- out: [index]
+ index:
+ run: kallisto-index.cwl
+ in:
+ InputFiles: IndexInput
+ IndexName:
+ source: IndexInput
+ valueFrom: $(self[0].nameroot)
+ out: [index]
- quant:
- run: kallisto-quant.cwl
- scatter: [InputReads, QuantOutfolder]
- scatterMethod: dotproduct
- in:
- InputReads:
- source: sampleRecord
- valueFrom: $(self.readsOfOneSample)
- QuantOutfolder:
- source: sampleRecord
- valueFrom: $(self.sampleName)
- Index: index/index
- isSingle: isSingle
- FragmentLength: FragmentLength
- StandardDeviation: StandardDeviation
- BootstrapSamples: BootstrapSamples
- out: [outFolder]
-
- collectResults:
- run: ./yield-dirInDestination.cwl
- scatter: inDir
- in:
- inDir: quant/outFolder
- destinationDir: resultsFolder
- out: [outDir]
+ quant:
+ run: kallisto-quant.cwl
+ scatter: [InputReads, QuantOutfolder]
+ scatterMethod: dotproduct
+ in:
+ InputReads:
+ source: sampleRecord
+ valueFrom: $(self.readsOfOneSample)
+ QuantOutfolder:
+ source: sampleRecord
+ valueFrom: $(self.sampleName)
+ Index: index/index
+ isSingle: isSingle
+ FragmentLength: FragmentLength
+ StandardDeviation: StandardDeviation
+ BootstrapSamples: BootstrapSamples
+ out: [kallistoQuantOutDir]
+ collectResults:
+ run: ./gather-dirs.cwl
+ in:
+ inDirs: quant/kallistoQuantOutDir
+ destinationDir: resultsFolder
+ out: [outDir]
outputs:
- finalOut:
- type: Directory[]
+ kallistoOutDir:
+ type: Directory
outputSource: collectResults/outDir
+
diff --git a/workflows/kallisto/yield-dirInDestination.cwl b/workflows/kallisto/yield-dirInDestination.cwl
deleted file mode 100644
index bc90cb81f1a907735bd433d6117c55872c213f92..0000000000000000000000000000000000000000
--- a/workflows/kallisto/yield-dirInDestination.cwl
+++ /dev/null
@@ -1,19 +0,0 @@
-cwlVersion: v1.2
-class: ExpressionTool
-doc: |
- Takes a directory (e.g. from a workflow step) and yields it in a desired directory.
-requirements:
- - class: InlineJavascriptRequirement
-inputs:
- inDir: Directory
- destinationDir: string
-expression: |
- ${
- return {"outDir": {
- "class": "Directory",
- "basename": inputs.destinationDir,
- "listing": [inputs.inDir]
- } };
- }
-outputs:
- outDir: Directory
\ No newline at end of file