From 1d5ac604da3b4a7f15961f2935d53d935666148d Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Tue, 18 Mar 2025 08:30:46 +0100
Subject: [PATCH] remove deprecated
---
workflows/kallisto/README.md | 12 --
.../{kallisto-help.cwl => kallisto-test.cwl} | 0
.../kallisto/kallisto_workflow_graph.svg | 173 ------------------
workflows/kallisto/yield-dirInDestination.cwl | 2 +-
4 files changed, 1 insertion(+), 186 deletions(-)
delete mode 100644 workflows/kallisto/README.md
rename workflows/kallisto/{kallisto-help.cwl => kallisto-test.cwl} (100%)
delete mode 100644 workflows/kallisto/kallisto_workflow_graph.svg
diff --git a/workflows/kallisto/README.md b/workflows/kallisto/README.md
deleted file mode 100644
index 244a3c1..0000000
--- a/workflows/kallisto/README.md
+++ /dev/null
@@ -1,12 +0,0 @@
-
-# Kallisto
-
-CWL adapted from: https://github.com/common-workflow-library/bio-cwl-tools/commit/91c42fb809ce18eafe16155cca0abf362270c0fe
-
-## Workflow graph
-
-```bash
-cwltool --print-dot kallisto-workflow.cwl | dot -Tsvg > kallisto_workflow_graph.svg
-```
-
-
\ No newline at end of file
diff --git a/workflows/kallisto/kallisto-help.cwl b/workflows/kallisto/kallisto-test.cwl
similarity index 100%
rename from workflows/kallisto/kallisto-help.cwl
rename to workflows/kallisto/kallisto-test.cwl
diff --git a/workflows/kallisto/kallisto_workflow_graph.svg b/workflows/kallisto/kallisto_workflow_graph.svg
deleted file mode 100644
index a9083ce..0000000
--- a/workflows/kallisto/kallisto_workflow_graph.svg
+++ /dev/null
@@ -1,173 +0,0 @@
-<?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 2.50.0 (20220117.2223)
- -->
-<!-- Title: G Pages: 1 -->
-<svg width="1313pt" height="395pt"
- viewBox="0.00 0.00 1313.00 395.00" 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(4 391)">
-<title>G</title>
-<polygon fill="#eeeeee" stroke="transparent" points="-4,4 -4,-391 1309,-391 1309,4 -4,4"/>
-<g id="clust1" class="cluster">
-<title>cluster_inputs</title>
-<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="8,-303 8,-379 1297,-379 1297,-303 8,-303"/>
-<text text-anchor="middle" x="1230" y="-310.8" 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="310,-8 310,-84 456,-84 456,-8 310,-8"/>
-<text text-anchor="middle" x="383" y="-15.8" font-family="Times,serif" font-size="14.00">Workflow Outputs</text>
-</g>
-<!-- quant -->
-<g id="node1" class="node">
-<title>quant</title>
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-<text text-anchor="middle" x="676" y="-199.8" font-family="Times,serif" font-size="14.00">quant</text>
-</g>
-<!-- collectResults -->
-<g id="node2" class="node">
-<title>collectResults</title>
-<polygon fill="lightgoldenrodyellow" stroke="black" points="325,-112.5 325,-148.5 441,-148.5 441,-112.5 325,-112.5"/>
-<text text-anchor="middle" x="383" y="-126.8" font-family="Times,serif" font-size="14.00">collectResults</text>
-</g>
-<!-- quant->collectResults -->
-<g id="edge1" class="edge">
-<title>quant->collectResults</title>
-<path fill="none" stroke="black" d="M646.83,-195.43C601.59,-184.47 513.24,-163.06 451.29,-148.05"/>
-<polygon fill="black" stroke="black" points="451.75,-144.56 441.2,-145.6 450.1,-151.36 451.75,-144.56"/>
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-<!-- finalOut -->
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-<title>finalOut</title>
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-<text text-anchor="middle" x="383" y="-53.8" font-family="Times,serif" font-size="14.00">finalOut</text>
-</g>
-<!-- collectResults->finalOut -->
-<g id="edge13" class="edge">
-<title>collectResults->finalOut</title>
-<path fill="none" stroke="black" d="M383,-112.31C383,-104.29 383,-94.55 383,-85.57"/>
-<polygon fill="black" stroke="black" points="386.5,-85.53 383,-75.53 379.5,-85.53 386.5,-85.53"/>
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-<!-- index -->
-<g id="node3" class="node">
-<title>index</title>
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-<text text-anchor="middle" x="194" y="-272.8" font-family="Times,serif" font-size="14.00">index</text>
-</g>
-<!-- index->quant -->
-<g id="edge2" class="edge">
-<title>index->quant</title>
-<path fill="none" stroke="black" d="M222.35,-271.32C304.43,-259.23 542.41,-224.18 636.78,-210.28"/>
-<polygon fill="black" stroke="black" points="637.39,-213.73 646.77,-208.81 636.37,-206.8 637.39,-213.73"/>
-</g>
-<!-- resultsFolder -->
-<g id="node4" class="node">
-<title>resultsFolder</title>
-<polygon fill="#94ddf4" stroke="black" points="16,-334.5 16,-370.5 128,-370.5 128,-334.5 16,-334.5"/>
-<text text-anchor="middle" x="72" y="-348.8" font-family="Times,serif" font-size="14.00">resultsFolder</text>
-</g>
-<!-- resultsFolder->collectResults -->
-<g id="edge3" class="edge">
-<title>resultsFolder->collectResults</title>
-<path fill="none" stroke="black" d="M84.72,-334.44C100.23,-314.43 127.98,-281.07 157,-258 213.1,-213.41 286.94,-175.31 334.69,-152.9"/>
-<polygon fill="black" stroke="black" points="336.29,-156.02 343.88,-148.63 333.34,-149.67 336.29,-156.02"/>
-</g>
-<!-- IndexInput -->
-<g id="node5" class="node">
-<title>IndexInput</title>
-<polygon fill="#94ddf4" stroke="black" points="146.5,-334.5 146.5,-370.5 241.5,-370.5 241.5,-334.5 146.5,-334.5"/>
-<text text-anchor="middle" x="194" y="-348.8" font-family="Times,serif" font-size="14.00">IndexInput</text>
-</g>
-<!-- IndexInput->index -->
-<g id="edge4" class="edge">
-<title>IndexInput->index</title>
-<path fill="none" stroke="black" d="M188.2,-334.34C187.27,-325.56 187.02,-314.66 187.46,-304.77"/>
-<polygon fill="black" stroke="black" points="190.97,-304.8 188.21,-294.57 183.99,-304.29 190.97,-304.8"/>
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-<!-- IndexInput->index -->
-<g id="edge5" class="edge">
-<title>IndexInput->index</title>
-<path fill="none" stroke="black" d="M199.8,-334.34C200.73,-325.56 200.98,-314.66 200.54,-304.77"/>
-<polygon fill="black" stroke="black" points="204.01,-304.29 199.79,-294.57 197.03,-304.8 204.01,-304.29"/>
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-<!-- BootstrapSamples -->
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-<title>BootstrapSamples</title>
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-<text text-anchor="middle" x="334" y="-348.8" font-family="Times,serif" font-size="14.00">BootstrapSamples</text>
-</g>
-<!-- BootstrapSamples->quant -->
-<g id="edge6" class="edge">
-<title>BootstrapSamples->quant</title>
-<path fill="none" stroke="black" d="M361.03,-334.43C377.21,-324.58 398.38,-312.33 418,-303 493.49,-267.08 585.84,-234.39 637.06,-217.2"/>
-<polygon fill="black" stroke="black" points="638.36,-220.46 646.74,-213.97 636.15,-213.81 638.36,-220.46"/>
-</g>
-<!-- FragmentLength -->
-<g id="node7" class="node">
-<title>FragmentLength</title>
-<polygon fill="#94ddf4" stroke="black" points="426.5,-334.5 426.5,-370.5 563.5,-370.5 563.5,-334.5 426.5,-334.5"/>
-<text text-anchor="middle" x="495" y="-348.8" font-family="Times,serif" font-size="14.00">FragmentLength</text>
-</g>
-<!-- FragmentLength->quant -->
-<g id="edge7" class="edge">
-<title>FragmentLength->quant</title>
-<path fill="none" stroke="black" d="M516.12,-334.35C548.54,-308.02 610.66,-257.56 647.19,-227.9"/>
-<polygon fill="black" stroke="black" points="649.46,-230.56 655.02,-221.54 645.05,-225.13 649.46,-230.56"/>
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-<!-- StandardDeviation -->
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-<title>StandardDeviation</title>
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-</g>
-<!-- StandardDeviation->quant -->
-<g id="edge8" class="edge">
-<title>StandardDeviation->quant</title>
-<path fill="none" stroke="black" d="M659.22,-334.35C662.48,-309.12 668.6,-261.76 672.48,-231.74"/>
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-<!-- isSingle -->
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-<title>isSingle</title>
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-<!-- isSingle->quant -->
-<g id="edge9" class="edge">
-<title>isSingle->quant</title>
-<path fill="none" stroke="black" d="M775.14,-334.23C766.7,-323.94 754.87,-311.31 742,-303 732.91,-297.13 727.06,-302.23 719,-295 700.25,-278.19 688.96,-251.45 682.68,-231.39"/>
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-</g>
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-<title>numUnderscoresFileName->quant</title>
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-<title>InputReadsMultipleSamples</title>
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-<title>InputReadsMultipleSamples->quant</title>
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-<title>InputReadsMultipleSamples->quant</title>
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diff --git a/workflows/kallisto/yield-dirInDestination.cwl b/workflows/kallisto/yield-dirInDestination.cwl
index c2a20ea..bc90cb8 100644
--- a/workflows/kallisto/yield-dirInDestination.cwl
+++ b/workflows/kallisto/yield-dirInDestination.cwl
@@ -1,7 +1,7 @@
cwlVersion: v1.2
class: ExpressionTool
doc: |
- Takes a directory (e.g. from a workflow step) and yield it in a desired directory.
+ Takes a directory (e.g. from a workflow step) and yields it in a desired directory.
requirements:
- class: InlineJavascriptRequirement
inputs:
--
GitLab