From 1fc1206b3be2e9061df4f2592111278e0ec82fb4 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Thu, 27 Mar 2025 22:36:41 +0100
Subject: [PATCH] add cwl aux as submodule
---
.cwl | 1 +
.cwl/README.md | 81 ------
.cwl/arc-cwl.svg | 245 ------------------
.cwl/cwl-metadata-checklist.md | 80 ------
.cwl/cwl-plots/plot-cwls.sh | 17 --
.cwl/cwl-plots/plot-runs.yml | 6 -
.cwl/cwl-plots/plot-workflows.yml | 6 -
.cwl/cwl-plots/plot.cwl | 85 ------
.cwl/cwl-plots/runs-wfls.txt | 6 -
.cwl/cwl-plots/runs/deseq2.svg | 89 -------
.cwl/cwl-plots/runs/fastqc.svg | 65 -----
.cwl/cwl-plots/runs/isaSampleToRawDataSeq.svg | 89 -------
.cwl/cwl-plots/runs/kallisto.svg | 125 ---------
.cwl/cwl-plots/runs/shiny.svg | 48 ----
.cwl/cwl-plots/runs/sleuth.svg | 113 --------
.cwl/cwl-plots/workflows/deseq2.svg | 0
.cwl/cwl-plots/workflows/fastqc.svg | 83 ------
.../workflows/isaSampleToRawDataSeq.svg | 0
.cwl/cwl-plots/workflows/kallisto.svg | 161 ------------
.cwl/cwl-plots/workflows/shiny.svg | 0
.cwl/cwl-plots/workflows/sleuth.svg | 0
.cwl/cwl-validation/validate-runs.txt | 36 ---
.cwl/cwl-validation/validate-runs.yml | 6 -
.cwl/cwl-validation/validate-workflows.txt | 36 ---
.cwl/cwl-validation/validate-workflows.yml | 6 -
.cwl/cwl-validation/validate.cwl | 47 ----
.gitmodules | 3 +
27 files changed, 4 insertions(+), 1430 deletions(-)
create mode 160000 .cwl
delete mode 100644 .cwl/README.md
delete mode 100644 .cwl/arc-cwl.svg
delete mode 100644 .cwl/cwl-metadata-checklist.md
delete mode 100644 .cwl/cwl-plots/plot-cwls.sh
delete mode 100644 .cwl/cwl-plots/plot-runs.yml
delete mode 100644 .cwl/cwl-plots/plot-workflows.yml
delete mode 100644 .cwl/cwl-plots/plot.cwl
delete mode 100644 .cwl/cwl-plots/runs-wfls.txt
delete mode 100644 .cwl/cwl-plots/runs/deseq2.svg
delete mode 100644 .cwl/cwl-plots/runs/fastqc.svg
delete mode 100644 .cwl/cwl-plots/runs/isaSampleToRawDataSeq.svg
delete mode 100644 .cwl/cwl-plots/runs/kallisto.svg
delete mode 100644 .cwl/cwl-plots/runs/shiny.svg
delete mode 100644 .cwl/cwl-plots/runs/sleuth.svg
delete mode 100644 .cwl/cwl-plots/workflows/deseq2.svg
delete mode 100644 .cwl/cwl-plots/workflows/fastqc.svg
delete mode 100644 .cwl/cwl-plots/workflows/isaSampleToRawDataSeq.svg
delete mode 100644 .cwl/cwl-plots/workflows/kallisto.svg
delete mode 100644 .cwl/cwl-plots/workflows/shiny.svg
delete mode 100644 .cwl/cwl-plots/workflows/sleuth.svg
delete mode 100644 .cwl/cwl-validation/validate-runs.txt
delete mode 100644 .cwl/cwl-validation/validate-runs.yml
delete mode 100644 .cwl/cwl-validation/validate-workflows.txt
delete mode 100644 .cwl/cwl-validation/validate-workflows.yml
delete mode 100644 .cwl/cwl-validation/validate.cwl
create mode 100644 .gitmodules
diff --git a/.cwl b/.cwl
new file mode 160000
index 0000000..568c3cf
--- /dev/null
+++ b/.cwl
@@ -0,0 +1 @@
+Subproject commit 568c3cf396dc8f6f9adfa3f7338805bb58379326
diff --git a/.cwl/README.md b/.cwl/README.md
deleted file mode 100644
index 0340cec..0000000
--- a/.cwl/README.md
+++ /dev/null
@@ -1,81 +0,0 @@
-# CWL
-
-**Data analysis** in this ARC is packaged and made reusable via [Common Workflow Language (CWL)](https://www.commonwl.org).
-For details, visit the [DataPLANT knowledgebase](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/cwl/).
-
-Briefly, every data analysis step (`runs`) is described with a `run.cwl` document. The `run.cwl` points (i.e. executes) one or multiple `workflows` (stored as `workflow.cwl`). The input parameters required for the `workflow.cwl` are documented in the accompanying `run.yml`. A `workflow.cwl` can be a single command line tool or a more complex workflow pipeline that references and combines other `*.cwl` documents.
-
-```bash
-...
-├── runs
-│ ├── fastqc
-│ │ ├── run.cwl
-│ │ └── run.yml
-│ ...
-├── studies
-│ ├── ...
-│
-└── workflows
- ├── fastqc
- │ ├── collectFilesInDir.cwl
- │ ├── fastqc.cwl
- │ └── workflow.cwl
- ...
-```
-
-```mermaid
-flowchart TD
-workflowcwl --- runcwl
-subgraph r["runs/fastqc/"]
- runcwl(("run.cwl"))
- runyml(("run.yml"))
-end
-i[input: DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz] --- runyml
-r ---> o[output: DB_097_CAMMD_CAGATC_L001_R1_001_fastqc.html]
-subgraph "workflows/fastqc"
- workflowcwl(("workflow.cwl"))
-end
-```
-
-
-## Setup and dependencies
-
-Again, for details check the docs linked above.
-Executing cwl documents requires a cwl runner, e.g. [cwltool](https://github.com/common-workflow-language/cwltool).
-Software and package dependencies are ideally covered by Docker or Conda and described in the hints / requirements sections of cwl documents (e.g. `DockerRequirement` and / or `SoftwareRequirement`).
-
-Additional dependencies may exist for one or the other workflow (e.g. a local installation of R or F# or packages therein), if the workflow is not yet packaged perfectly reusable.
-
-## Default cwltool commands
-
-Here's a list of frequently used `cwltool` commands to validate or execute runs and workflows.
-
-### Validate document
-
-```bash
-cwltool --validate run.cwl
-```
-
-### Execute workflow in `./runs/*`
-
-```bash
-cwltool run.cwl run.yml
-```
-
-### capture log and run in bg
-
-```bash
-cwltool run.cwl run.yml > $(date +"%Y-%m-%d_%H-%M")-run.log 2>&1 &
-```
-
-### capture log, run in parallel and in bg
-
-```bash
-cwltool --parallel run.cwl run.yml > $(date +"%Y-%m-%d_%H-%M")-run.log 2>&1 &
-```
-
-### Print workflow to file
-
-```bash
-cwltool --print-dot ../arc.cwl | dot -Tsvg > arc-cwl.svg
-```
diff --git a/.cwl/arc-cwl.svg b/.cwl/arc-cwl.svg
deleted file mode 100644
index 8269aa8..0000000
--- a/.cwl/arc-cwl.svg
+++ /dev/null
@@ -1,245 +0,0 @@
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-<title>G</title>
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-<g id="clust2" class="cluster">
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-<title>kallisto->sleuth</title>
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-<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>
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-<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>
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diff --git a/.cwl/cwl-metadata-checklist.md b/.cwl/cwl-metadata-checklist.md
deleted file mode 100644
index e7b070f..0000000
--- a/.cwl/cwl-metadata-checklist.md
+++ /dev/null
@@ -1,80 +0,0 @@
-
-# Checklist for good CWL documents
-
-based on recommendations from:
-
-- https://www.commonwl.org/user_guide/topics/best-practices.html
-- https://www.commonwl.org/user_guide/topics/metadata-and-authorship.html
-
-- [Design](#design)
- - [Single-step first](#single-step-first)
-- [Dependencies](#dependencies)
- - [Soft requirements = `hints`](#soft-requirements--hints)
- - [Hard requirements = `requirements`](#hard-requirements--requirements)
-- [Metadata](#metadata)
- - [Namespaces and schemas](#namespaces-and-schemas)
-
-## Design
-
-### Keep it Simple: Single-step
-
-- follow the [KISS principle](https://en.wikipedia.org/wiki/KISS_principle)
-- a `CommandLineTool` document should only execute one process
-- use `Workflow` documents to design more complex, multi-step pipelines
-- use `scatter` to execute the process on multiple inputs
-- do not hard code input, output paths
-
-## Dependencies
-
-### Soft requirements = `hints`
-
-Specify software and resource requirements under `hints`
-
-- add `SoftwareRequirement` to specify software version and reference
- - `package: ` name of the software or package
- - `specs: ` reference url from https://identifiers.org/biotools/ or SciCrunch https://identifiers.org/rrid/
- - `version: [ "0.11.9" ]`
-- add `DockerRequirement`
- - reference a local `Dockerfile` or a published Docker image
-- add `ResourceRequirement` to specify the required compute resources
-
-### Hard requirements = `requirements`
-
-Use the `requirements` primarily to specify hard requirements needed to run the current `CommandLineTool` or `Workflow` document
-
-## Metadata
-
-### Namespaces and schemas
-
-Adding namespaces and schemas allows to reuse them elsewhere in a CWL document
-
-```yaml
-$namespaces:
- s: https://schema.org/
- edam: http://edamontology.org/
-
-$schemas:
- - https://schema.org/version/latest/schemaorg-current-https.rdf
- - http://edamontology.org/EDAM_1.18.owl
-```
-
-### Attribute authors and contributors
-
-```yaml
-s:author:
- - class: s:Person
- s:identifier: <author ORCID>
- s:email: mailto:<author email>
- s:name: <author name>
-
-s:contributor:
- - class: s:Person
- s:identifier: <contributor ORCID>
- s:email: mailto:<contributor email>
- s:name: <contributor name>
-
-s:citation: <DOI to software paper>
-s:codeRepository: <URL to software repo (e.g. github)>
-s:dateCreated: "2016-12-13"
-s:license: <URL to license, e.g. from https://spdx.org/licenses/>
-```
diff --git a/.cwl/cwl-plots/plot-cwls.sh b/.cwl/cwl-plots/plot-cwls.sh
deleted file mode 100644
index f78df0c..0000000
--- a/.cwl/cwl-plots/plot-cwls.sh
+++ /dev/null
@@ -1,17 +0,0 @@
-
-
-# Test : `bash plot-cwls.sh "../../" "run.cwl" "runs-wfls.txt" "runs"`
-
-arcRoot=$1
-cwlPattern=$2
-outWflList=$3
-outGraphs=$4
-
-find "$arcRoot"/ -name "$cwlPattern" > "$outWflList"
-
-mkdir -p "$outGraphs"
-
-while IFS= read -r wfl; do
- read wflname < <(dirname "$wfl" | xargs basename)
- cwltool --print-dot "$wfl" | dot -Tsvg > "$outGraphs"/"$wflname".svg
-done < "$outWflList"
\ No newline at end of file
diff --git a/.cwl/cwl-plots/plot-runs.yml b/.cwl/cwl-plots/plot-runs.yml
deleted file mode 100644
index 4fa1e6e..0000000
--- a/.cwl/cwl-plots/plot-runs.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-arcRoot:
- class: Directory
- path: "../../"
-cwlPattern: "run.cwl"
-outWflList: "runs-wfls.txt"
-outGraphs: "runs"
\ No newline at end of file
diff --git a/.cwl/cwl-plots/plot-workflows.yml b/.cwl/cwl-plots/plot-workflows.yml
deleted file mode 100644
index f2eaecb..0000000
--- a/.cwl/cwl-plots/plot-workflows.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-arcRoot:
- class: Directory
- path: "../../"
-cwlPattern: "workflow.cwl"
-outWflList: "workflow-wfls.txt"
-outGraphs: "workflows"
\ No newline at end of file
diff --git a/.cwl/cwl-plots/plot.cwl b/.cwl/cwl-plots/plot.cwl
deleted file mode 100644
index 799d219..0000000
--- a/.cwl/cwl-plots/plot.cwl
+++ /dev/null
@@ -1,85 +0,0 @@
-#!/usr/bin/env cwl-runner
-cwlVersion: v1.2
-class: Workflow
-
-inputs:
- arcRoot:
- type: Directory
- cwlPattern:
- type: string
- outWflList:
- type: string
- outGraphs:
- type: string
-
-outputs:
- outputDir:
- type: Directory
- outputSource: collect_files/outDir
-
-steps:
- plot:
- run:
- class: CommandLineTool
- requirements:
- InitialWorkDirRequirement:
- listing:
- - entryname: plot-cwls.sh
- entry:
- $include: plot-cwls.sh
-
- baseCommand: ["bash", "plot-cwls.sh"]
-
- inputs:
- arcRoot:
- type: Directory
- inputBinding:
- position: 1
- cwlPattern:
- type: string
- inputBinding:
- position: 2
- outWflList:
- type: string
- inputBinding:
- position: 3
- outGraphs:
- type: string
- inputBinding:
- position: 4
-
- outputs:
- output_files:
- type: File[]
- outputBinding:
- glob: $(inputs.outGraphs)/*.svg
- in:
- arcRoot: arcRoot
- cwlPattern: cwlPattern
- outWflList: outWflList
- outGraphs: outGraphs
-
- out: [output_files]
-
- collect_files:
- run:
- class: ExpressionTool
- requirements:
- InlineJavascriptRequirement: {}
- inputs:
- files: File[]
- destination: string
- expression: |
- ${
- return {"outDir": {
- "class": "Directory",
- "basename": inputs.destination,
- "listing": inputs.files
- } };
- }
- outputs:
- outDir: Directory
- in:
- files: plot/output_files
- destination: outGraphs
- out: [outDir]
diff --git a/.cwl/cwl-plots/runs-wfls.txt b/.cwl/cwl-plots/runs-wfls.txt
deleted file mode 100644
index 32989c5..0000000
--- a/.cwl/cwl-plots/runs-wfls.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-../..///runs/shiny/run.cwl
-../..///runs/deseq2/run.cwl
-../..///runs/sleuth/run.cwl
-../..///runs/fastqc/run.cwl
-../..///runs/kallisto/run.cwl
-../..///runs/isaSampleToRawDataSeq/run.cwl
diff --git a/.cwl/cwl-plots/runs/deseq2.svg b/.cwl/cwl-plots/runs/deseq2.svg
deleted file mode 100644
index 29efcbd..0000000
--- a/.cwl/cwl-plots/runs/deseq2.svg
+++ /dev/null
@@ -1,89 +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">
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- -->
-<!-- Title: G Pages: 1 -->
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-<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 242)">
-<title>G</title>
-<polygon fill="#eeeeee" stroke="transparent" points="-4,4 -4,-242 560,-242 560,4 -4,4"/>
-<g id="clust1" class="cluster">
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-<text text-anchor="middle" x="492.92" y="-161.8" font-family="Times,serif" font-size="14.00">Workflow Inputs</text>
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-<text text-anchor="middle" x="273.25" y="-14.8" font-family="Times,serif" font-size="14.00">Workflow Outputs</text>
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-<!-- inKallistoResults -->
-<g id="node1" class="node">
-<title>inKallistoResults</title>
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-<text text-anchor="middle" x="273" y="-124.8" font-family="Times,serif" font-size="14.00">deseq2</text>
-</g>
-<!-- inKallistoResults->deseq2 -->
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-<title>inKallistoResults->deseq2</title>
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-<title>inMetadataFactorList->deseq2</title>
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-<!-- inMetadataFile->deseq2 -->
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-<title>inMetadataFile->deseq2</title>
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-</g>
-<!-- inMetadataSample->deseq2 -->
-<g id="edge4" class="edge">
-<title>inMetadataSample->deseq2</title>
-<path fill="none" stroke="black" d="M96.47,-185.35C109.78,-175.05 127.97,-162.52 146,-155 172.43,-143.97 204.02,-137.73 229.08,-134.24"/>
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-<g id="node6" class="node">
-<title>output</title>
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-</g>
-<!-- deseq2->output -->
-<g id="edge5" class="edge">
-<title>deseq2->output</title>
-<path fill="none" stroke="black" d="M273,-110.93C273,-103.17 273,-93.78 273,-85.06"/>
-<polygon fill="black" stroke="black" points="276.5,-84.9 273,-74.9 269.5,-84.9 276.5,-84.9"/>
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-</g>
-</svg>
diff --git a/.cwl/cwl-plots/runs/fastqc.svg b/.cwl/cwl-plots/runs/fastqc.svg
deleted file mode 100644
index 485ba4e..0000000
--- a/.cwl/cwl-plots/runs/fastqc.svg
+++ /dev/null
@@ -1,65 +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">
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-<!-- Title: G Pages: 1 -->
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-<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 242)">
-<title>G</title>
-<polygon fill="#eeeeee" stroke="transparent" points="-4,4 -4,-242 182,-242 182,4 -4,4"/>
-<g id="clust1" class="cluster">
-<title>cluster_inputs</title>
-<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="8,-155 8,-230 170,-230 170,-155 8,-155"/>
-<text text-anchor="middle" x="114.92" y="-161.8" 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="32,-8 32,-83 151,-83 151,-8 32,-8"/>
-<text text-anchor="middle" x="91.25" y="-14.8" font-family="Times,serif" font-size="14.00">Workflow Outputs</text>
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-<!-- fastq -->
-<g id="node1" class="node">
-<title>fastq</title>
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-<!-- fastqc -->
-<g id="node3" class="node">
-<title>fastqc</title>
-<ellipse fill="none" stroke="black" cx="72" cy="-129" rx="31.45" ry="18"/>
-<text text-anchor="middle" x="72" y="-124.8" 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="M123.03,-185.22C116.33,-175.95 107.62,-164.51 99,-155 97.98,-153.88 96.92,-152.74 95.83,-151.62"/>
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-<!-- finaloutdir -->
-<g id="node2" class="node">
-<title>finaloutdir</title>
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-<!-- finaloutdir->fastqc -->
-<g id="edge2" class="edge">
-<title>finaloutdir->fastqc</title>
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-<!-- outdir -->
-<g id="node4" class="node">
-<title>outdir</title>
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-<!-- fastqc->outdir -->
-<g id="edge3" class="edge">
-<title>fastqc->outdir</title>
-<path fill="none" stroke="black" d="M72,-110.93C72,-103.17 72,-93.78 72,-85.06"/>
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diff --git a/.cwl/cwl-plots/runs/isaSampleToRawDataSeq.svg b/.cwl/cwl-plots/runs/isaSampleToRawDataSeq.svg
deleted file mode 100644
index 6523ee3..0000000
--- a/.cwl/cwl-plots/runs/isaSampleToRawDataSeq.svg
+++ /dev/null
@@ -1,89 +0,0 @@
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-<title>G</title>
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-<g id="clust1" class="cluster">
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diff --git a/.cwl/cwl-plots/workflows/isaSampleToRawDataSeq.svg b/.cwl/cwl-plots/workflows/isaSampleToRawDataSeq.svg
deleted file mode 100644
index e69de29..0000000
diff --git a/.cwl/cwl-plots/workflows/kallisto.svg b/.cwl/cwl-plots/workflows/kallisto.svg
deleted file mode 100644
index 930b4ca..0000000
--- a/.cwl/cwl-plots/workflows/kallisto.svg
+++ /dev/null
@@ -1,161 +0,0 @@
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diff --git a/.cwl/cwl-plots/workflows/shiny.svg b/.cwl/cwl-plots/workflows/shiny.svg
deleted file mode 100644
index e69de29..0000000
diff --git a/.cwl/cwl-plots/workflows/sleuth.svg b/.cwl/cwl-plots/workflows/sleuth.svg
deleted file mode 100644
index e69de29..0000000
diff --git a/.cwl/cwl-validation/validate-runs.txt b/.cwl/cwl-validation/validate-runs.txt
deleted file mode 100644
index d6d9087..0000000
--- a/.cwl/cwl-validation/validate-runs.txt
+++ /dev/null
@@ -1,36 +0,0 @@
-------------------
-/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/shiny/run.cwl
-[1;30mINFO[0m /Users/dominikbrilhaus/miniconda3/bin/cwltool 3.1.20250110105449
-[1;30mINFO[0m Resolved '/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/shiny/run.cwl' to 'file:///private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum/runs/shiny/run.cwl'
-/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/shiny/run.cwl is valid CWL.
-------------------
-------------------
-/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/deseq2/run.cwl
-[1;30mINFO[0m /Users/dominikbrilhaus/miniconda3/bin/cwltool 3.1.20250110105449
-[1;30mINFO[0m Resolved '/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/deseq2/run.cwl' to 'file:///private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum/runs/deseq2/run.cwl'
-/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/deseq2/run.cwl is valid CWL.
-------------------
-------------------
-/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/sleuth/run.cwl
-[1;30mINFO[0m /Users/dominikbrilhaus/miniconda3/bin/cwltool 3.1.20250110105449
-[1;30mINFO[0m Resolved '/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/sleuth/run.cwl' to 'file:///private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum/runs/sleuth/run.cwl'
-/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/sleuth/run.cwl is valid CWL.
-------------------
-------------------
-/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/fastqc/run.cwl
-[1;30mINFO[0m /Users/dominikbrilhaus/miniconda3/bin/cwltool 3.1.20250110105449
-[1;30mINFO[0m Resolved '/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/fastqc/run.cwl' to 'file:///private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum/runs/fastqc/run.cwl'
-/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/fastqc/run.cwl is valid CWL.
-------------------
-------------------
-/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/kallisto/run.cwl
-[1;30mINFO[0m /Users/dominikbrilhaus/miniconda3/bin/cwltool 3.1.20250110105449
-[1;30mINFO[0m Resolved '/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/kallisto/run.cwl' to 'file:///private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum/runs/kallisto/run.cwl'
-/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/kallisto/run.cwl is valid CWL.
-------------------
-------------------
-/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/isaSampleToRawDataSeq/run.cwl
-[1;30mINFO[0m /Users/dominikbrilhaus/miniconda3/bin/cwltool 3.1.20250110105449
-[1;30mINFO[0m Resolved '/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/isaSampleToRawDataSeq/run.cwl' to 'file:///private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum/runs/isaSampleToRawDataSeq/run.cwl'
-/private/tmp/docker_tmpoqv_exup/stg8073d243-c2d6-4086-85a7-421652f1e9dd/Facultative-CAM-in-Talinum//runs/isaSampleToRawDataSeq/run.cwl is valid CWL.
-------------------
diff --git a/.cwl/cwl-validation/validate-runs.yml b/.cwl/cwl-validation/validate-runs.yml
deleted file mode 100644
index b5283d9..0000000
--- a/.cwl/cwl-validation/validate-runs.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-arcRoot:
- class: Directory
- path: "../../"
-cwlPattern: "run.cwl"
-outWflList: "runs-wfls.txt"
-outValidation: "validate-runs.txt"
\ No newline at end of file
diff --git a/.cwl/cwl-validation/validate-workflows.txt b/.cwl/cwl-validation/validate-workflows.txt
deleted file mode 100644
index 1f3eb29..0000000
--- a/.cwl/cwl-validation/validate-workflows.txt
+++ /dev/null
@@ -1,36 +0,0 @@
-------------------
-/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/shiny/workflow.cwl
-[1;30mINFO[0m /Users/dominikbrilhaus/miniconda3/bin/cwltool 3.1.20250110105449
-[1;30mINFO[0m Resolved '/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/shiny/workflow.cwl' to 'file:///private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum/workflows/shiny/workflow.cwl'
-/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/shiny/workflow.cwl is valid CWL.
-------------------
-------------------
-/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/deseq2/workflow.cwl
-[1;30mINFO[0m /Users/dominikbrilhaus/miniconda3/bin/cwltool 3.1.20250110105449
-[1;30mINFO[0m Resolved '/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/deseq2/workflow.cwl' to 'file:///private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum/workflows/deseq2/workflow.cwl'
-/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/deseq2/workflow.cwl is valid CWL.
-------------------
-------------------
-/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/sleuth/workflow.cwl
-[1;30mINFO[0m /Users/dominikbrilhaus/miniconda3/bin/cwltool 3.1.20250110105449
-[1;30mINFO[0m Resolved '/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/sleuth/workflow.cwl' to 'file:///private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum/workflows/sleuth/workflow.cwl'
-/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/sleuth/workflow.cwl is valid CWL.
-------------------
-------------------
-/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/fastqc/workflow.cwl
-[1;30mINFO[0m /Users/dominikbrilhaus/miniconda3/bin/cwltool 3.1.20250110105449
-[1;30mINFO[0m Resolved '/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/fastqc/workflow.cwl' to 'file:///private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum/workflows/fastqc/workflow.cwl'
-/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/fastqc/workflow.cwl is valid CWL.
-------------------
-------------------
-/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/kallisto/workflow.cwl
-[1;30mINFO[0m /Users/dominikbrilhaus/miniconda3/bin/cwltool 3.1.20250110105449
-[1;30mINFO[0m Resolved '/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/kallisto/workflow.cwl' to 'file:///private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum/workflows/kallisto/workflow.cwl'
-/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/kallisto/workflow.cwl is valid CWL.
-------------------
-------------------
-/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/isaSampleToRawDataSeq/workflow.cwl
-[1;30mINFO[0m /Users/dominikbrilhaus/miniconda3/bin/cwltool 3.1.20250110105449
-[1;30mINFO[0m Resolved '/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/isaSampleToRawDataSeq/workflow.cwl' to 'file:///private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum/workflows/isaSampleToRawDataSeq/workflow.cwl'
-/private/tmp/docker_tmpjlgidqrn/stg07ca2d65-dfb1-42a7-be80-dc41a26f65a4/Facultative-CAM-in-Talinum//workflows/isaSampleToRawDataSeq/workflow.cwl is valid CWL.
-------------------
diff --git a/.cwl/cwl-validation/validate-workflows.yml b/.cwl/cwl-validation/validate-workflows.yml
deleted file mode 100644
index ad62de6..0000000
--- a/.cwl/cwl-validation/validate-workflows.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-arcRoot:
- class: Directory
- path: "../../"
-cwlPattern: "workflow.cwl"
-outWflList: "workflow-wfls.txt"
-outValidation: "validate-workflows.txt"
\ No newline at end of file
diff --git a/.cwl/cwl-validation/validate.cwl b/.cwl/cwl-validation/validate.cwl
deleted file mode 100644
index 4b867ce..0000000
--- a/.cwl/cwl-validation/validate.cwl
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/usr/bin/env cwl-runner
-cwlVersion: v1.2
-class: CommandLineTool
-requirements:
- InitialWorkDirRequirement:
- listing:
- - entryname: validate-cwls.sh
- entry: |-
- arcRoot=$1
- cwlPattern=$2
- outWflList=$3
- outValidation=$4
-
- find "$arcRoot"/ -name "$cwlPattern" > "$outWflList"
-
- while IFS= read -r wfl; do
- printf '%s %s\n' "------------------" >> "$outValidation"
- printf '%s %s\n' "$wfl" >> "$outValidation"
- cwltool --validate "$wfl" >> "$outValidation"
- printf '%s %s\n' "------------------" >> "$outValidation"
- done < "$outWflList"
-
-baseCommand: ["bash", "validate-cwls.sh"]
-
-inputs:
- arcRoot:
- type: Directory
- inputBinding:
- position: 1
- cwlPattern:
- type: string
- inputBinding:
- position: 2
- outWflList:
- type: string
- inputBinding:
- position: 3
- outValidation:
- type: string
- inputBinding:
- position: 4
-
-stdout: $(inputs.outValidation)
-
-outputs:
- output_file:
- type: stdout
\ No newline at end of file
diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..24452bb
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule ".cwl"]
+ path = .cwl
+ url = https://git.nfdi4plants.org/brilator/cwl-aux.git
--
GitLab