From 2dbb8cc5c5b505abab5aa3d75b6f04e5d0b6515a Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Fri, 2 Aug 2024 16:22:20 +0200
Subject: [PATCH] kallisto workflow results all samples
---
.../kallisto_results/DB_097/abundance.h5 | 3 +
.../kallisto_results/DB_097/abundance.tsv | 3 +
.../kallisto_results/DB_097/run_info.json | 3 +
.../kallisto_results/DB_099/abundance.h5 | 3 +
.../kallisto_results/DB_099/abundance.tsv | 3 +
.../kallisto_results/DB_099/run_info.json | 3 +
.../kallisto_results/DB_103/abundance.h5 | 3 +
.../kallisto_results/DB_103/abundance.tsv | 3 +
.../kallisto_results/DB_103/run_info.json | 3 +
.../kallisto_results/DB_161/abundance.h5 | 3 +
.../kallisto_results/DB_161/abundance.tsv | 3 +
.../kallisto_results/DB_161/run_info.json | 3 +
.../kallisto_results/DB_163/abundance.h5 | 3 +
.../kallisto_results/DB_163/abundance.tsv | 3 +
.../kallisto_results/DB_163/run_info.json | 3 +
.../kallisto_results/DB_165/abundance.h5 | 3 +
.../kallisto_results/DB_165/abundance.tsv | 3 +
.../kallisto_results/DB_165/run_info.json | 3 +
runs/kallisto/workflow.yml | 30 +++-
workflows/kallisto/README.md | 7 +-
workflows/kallisto/kallisto-workflow.cwl | 4 +-
.../kallisto/kallisto_workflow_graph.svg | 161 ++++++++++++++++++
22 files changed, 245 insertions(+), 11 deletions(-)
create mode 100644 runs/kallisto/kallisto_results/DB_097/abundance.h5
create mode 100644 runs/kallisto/kallisto_results/DB_097/abundance.tsv
create mode 100644 runs/kallisto/kallisto_results/DB_097/run_info.json
create mode 100644 runs/kallisto/kallisto_results/DB_099/abundance.h5
create mode 100644 runs/kallisto/kallisto_results/DB_099/abundance.tsv
create mode 100644 runs/kallisto/kallisto_results/DB_099/run_info.json
create mode 100644 runs/kallisto/kallisto_results/DB_103/abundance.h5
create mode 100644 runs/kallisto/kallisto_results/DB_103/abundance.tsv
create mode 100644 runs/kallisto/kallisto_results/DB_103/run_info.json
create mode 100644 runs/kallisto/kallisto_results/DB_161/abundance.h5
create mode 100644 runs/kallisto/kallisto_results/DB_161/abundance.tsv
create mode 100644 runs/kallisto/kallisto_results/DB_161/run_info.json
create mode 100644 runs/kallisto/kallisto_results/DB_163/abundance.h5
create mode 100644 runs/kallisto/kallisto_results/DB_163/abundance.tsv
create mode 100644 runs/kallisto/kallisto_results/DB_163/run_info.json
create mode 100644 runs/kallisto/kallisto_results/DB_165/abundance.h5
create mode 100644 runs/kallisto/kallisto_results/DB_165/abundance.tsv
create mode 100644 runs/kallisto/kallisto_results/DB_165/run_info.json
create mode 100644 workflows/kallisto/kallisto_workflow_graph.svg
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diff --git a/runs/kallisto/kallisto_results/DB_099/abundance.tsv b/runs/kallisto/kallisto_results/DB_099/abundance.tsv
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diff --git a/runs/kallisto/kallisto_results/DB_165/abundance.tsv b/runs/kallisto/kallisto_results/DB_165/abundance.tsv
new file mode 100644
index 0000000..2be2791
--- /dev/null
+++ b/runs/kallisto/kallisto_results/DB_165/abundance.tsv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 958459
diff --git a/runs/kallisto/kallisto_results/DB_165/run_info.json b/runs/kallisto/kallisto_results/DB_165/run_info.json
new file mode 100644
index 0000000..0f49f0c
--- /dev/null
+++ b/runs/kallisto/kallisto_results/DB_165/run_info.json
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 561
diff --git a/runs/kallisto/workflow.yml b/runs/kallisto/workflow.yml
index 44b12a5..65f21a5 100644
--- a/runs/kallisto/workflow.yml
+++ b/runs/kallisto/workflow.yml
@@ -13,20 +13,34 @@ InputReadsMultipleSamples:
- class: File
path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
format: edam:format_1930 # FASTQ
- # -
- # - class: File
- # path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
- # format: edam:format_1930 # FASTQ
-
-numCharsFastqFileName: 6
+ -
+ - class: File
+ path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
+ format: edam:format_1930 # FASTQ
+ -
+ - class: File
+ path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
+ format: edam:format_1930 # FASTQ
+ -
+ - class: File
+ path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
+ format: edam:format_1930 # FASTQ
+ -
+ - class: File
+ path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
+ format: edam:format_1930 # FASTQ
+ -
+ - class: File
+ path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
+ format: edam:format_1930 # FASTQ
### Kallisto quant Parameters
isSingle: true
FragmentLength: 200
StandardDeviation: 20
-BootstrapSamples: 1
+BootstrapSamples: 30
-resultsFolder: kallist_results
+resultsFolder: kallisto_results
$namespaces:
edam: https://edamontology.org/
\ No newline at end of file
diff --git a/workflows/kallisto/README.md b/workflows/kallisto/README.md
index 52f46ea..244a3c1 100644
--- a/workflows/kallisto/README.md
+++ b/workflows/kallisto/README.md
@@ -1,7 +1,12 @@
# Kallisto
+CWL adapted from: https://github.com/common-workflow-library/bio-cwl-tools/commit/91c42fb809ce18eafe16155cca0abf362270c0fe
+## Workflow graph
-CWL adapted from: https://github.com/common-workflow-library/bio-cwl-tools/commit/91c42fb809ce18eafe16155cca0abf362270c0fe
+```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-workflow.cwl b/workflows/kallisto/kallisto-workflow.cwl
index 6bbeb9d..8a94523 100644
--- a/workflows/kallisto/kallisto-workflow.cwl
+++ b/workflows/kallisto/kallisto-workflow.cwl
@@ -52,9 +52,9 @@ steps:
in:
inDir: quant/outFolder
destinationDir: resultsFolder
- out: outDir
+ out: [outDir]
outputs:
finalOut:
- type: Directory
+ type: Directory[]
outputSource: collectResults/outDir
diff --git a/workflows/kallisto/kallisto_workflow_graph.svg b/workflows/kallisto/kallisto_workflow_graph.svg
new file mode 100644
index 0000000..1eb967f
--- /dev/null
+++ b/workflows/kallisto/kallisto_workflow_graph.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 2.50.0 (0)
+ -->
+<!-- Title: G Pages: 1 -->
+<svg width="886pt" height="395pt"
+ viewBox="0.00 0.00 886.00 395.00" 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,-391 882,-391 882,4 -4,4"/>
+<g id="clust1" class="cluster">
+<title>cluster_inputs</title>
+<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="8,-303 8,-379 870,-379 870,-303 8,-303"/>
+<text text-anchor="middle" x="815" 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="228,-8 228,-84 347,-84 347,-8 228,-8"/>
+<text text-anchor="middle" x="287.5" y="-15.8" font-family="Times,serif" font-size="14.00">Workflow Outputs</text>
+</g>
+<!-- quant -->
+<g id="node1" class="node">
+<title>quant</title>
+<polygon fill="lightgoldenrodyellow" stroke="black" points="484,-185.5 484,-221.5 538,-221.5 538,-185.5 484,-185.5"/>
+<text text-anchor="middle" x="511" 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="241,-112.5 241,-148.5 333,-148.5 333,-112.5 241,-112.5"/>
+<text text-anchor="middle" x="287" 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="M483.98,-193.94C449.18,-182.91 387.83,-163.46 342.82,-149.19"/>
+<polygon fill="black" stroke="black" points="343.78,-145.83 333.19,-146.14 341.67,-152.5 343.78,-145.83"/>
+</g>
+<!-- finalOut -->
+<g id="node11" class="node">
+<title>finalOut</title>
+<polygon fill="#94ddf4" stroke="black" points="256,-39.5 256,-75.5 318,-75.5 318,-39.5 256,-39.5"/>
+<text text-anchor="middle" x="287" y="-53.8" font-family="Times,serif" font-size="14.00">finalOut</text>
+</g>
+<!-- collectResults->finalOut -->
+<g id="edge12" class="edge">
+<title>collectResults->finalOut</title>
+<path fill="none" stroke="black" d="M287,-112.31C287,-104.29 287,-94.55 287,-85.57"/>
+<polygon fill="black" stroke="black" points="290.5,-85.53 287,-75.53 283.5,-85.53 290.5,-85.53"/>
+</g>
+<!-- index -->
+<g id="node3" class="node">
+<title>index</title>
+<polygon fill="lightgoldenrodyellow" stroke="black" points="133,-258.5 133,-294.5 187,-294.5 187,-258.5 133,-258.5"/>
+<text text-anchor="middle" x="160" 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="M187.25,-269.99C249.58,-257.38 402.63,-226.42 473.66,-212.05"/>
+<polygon fill="black" stroke="black" points="474.42,-215.47 483.53,-210.06 473.03,-208.61 474.42,-215.47"/>
+</g>
+<!-- resultsFolder -->
+<g id="node4" class="node">
+<title>resultsFolder</title>
+<polygon fill="#94ddf4" stroke="black" points="16.5,-334.5 16.5,-370.5 103.5,-370.5 103.5,-334.5 16.5,-334.5"/>
+<text text-anchor="middle" x="60" 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="M69.46,-334.48C80.86,-314.81 101.34,-282.06 124,-258 163.17,-216.42 216.8,-177.55 251.67,-154.15"/>
+<polygon fill="black" stroke="black" points="253.71,-156.99 260.11,-148.54 249.84,-151.16 253.71,-156.99"/>
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+<!-- IndexInput -->
+<g id="node5" class="node">
+<title>IndexInput</title>
+<polygon fill="#94ddf4" stroke="black" points="122,-334.5 122,-370.5 198,-370.5 198,-334.5 122,-334.5"/>
+<text text-anchor="middle" x="160" 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="M154.2,-334.34C153.27,-325.56 153.02,-314.66 153.46,-304.77"/>
+<polygon fill="black" stroke="black" points="156.97,-304.8 154.21,-294.57 149.99,-304.29 156.97,-304.8"/>
+</g>
+<!-- IndexInput->index -->
+<g id="edge5" class="edge">
+<title>IndexInput->index</title>
+<path fill="none" stroke="black" d="M165.8,-334.34C166.73,-325.56 166.98,-314.66 166.54,-304.77"/>
+<polygon fill="black" stroke="black" points="170.01,-304.29 165.79,-294.57 163.03,-304.8 170.01,-304.29"/>
+</g>
+<!-- BootstrapSamples -->
+<g id="node6" class="node">
+<title>BootstrapSamples</title>
+<polygon fill="#94ddf4" stroke="black" points="216,-334.5 216,-370.5 332,-370.5 332,-334.5 216,-334.5"/>
+<text text-anchor="middle" x="274" 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="M296.92,-334.35C309.94,-324.82 326.65,-312.92 342,-303 386.91,-273.99 440.49,-243.41 475.1,-224.16"/>
+<polygon fill="black" stroke="black" points="476.86,-227.19 483.91,-219.28 473.46,-221.07 476.86,-227.19"/>
+</g>
+<!-- FragmentLength -->
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--
GitLab