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Commit 7943aba7 authored by Dominik Brilhaus's avatar Dominik Brilhaus
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Merge branch 'cwl' into 'main' 

Cwl

See merge request !16
parents b6cbec3a 1579a8e9
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1 merge request!16Cwl
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Stage: arc_json
    Stage: quality_report_generator
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        .cwl/README.md 0 → 100644
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        # 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
        %%{ init: {"flowchart": { "wrappingWidth": "10000" }}}%%
        flowchart TD
        workflowcwl --o runcwl
        subgraph r["runs/fastqc/"]
        runcwl@{ shape: doc, label: "run.cwl" }
        runyml@{ shape: doc, label: "run.yml" }
        end
        i[input: DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz] --o runyml
        r --> o[output: DB_097_CAMMD_CAGATC_L001_R1_001_fastqc.html]
        subgraph "workflows/fastqc"
        workflowcwl@{ shape: doc, label: "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 run.cwl | dot -Tsvg > run.svg
        ```
        .cwl/cwl-notes.md deleted 100644 → 0
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        # CWL
        ## Organisation
        ### Runs
        Every run is described with a `run.cwl` workflow that points to (i.e. steps through) one or multiple workflows or tools.
        ## Default cwltool commands
        ### 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 run.cwl | dot -Tsvg > run.svg
        ```
        ### List all workflows
        ```bash
        find ./workflows -name 'workflow.cwl' -exec zsh -c 'echo "$1" >> workflows.txt' zsh {} \;
        find ./workflows -name 'workflow.cwl' -exec zsh -c 'cwltool --validate "$1" > validate-workflows.txt' zsh {} \;
        find ./runs -name 'run.cwl' -exec zsh -c 'cwltool --validate "$1" > validate-runs.txt' zsh {} \;
        ```
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        ```bash
        bash plot-cwls.sh "../../" "run.cwl" "runs-wfls.txt" "runs"
        ```
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        .cwl/cwl-plots/plot-cwls.sh
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        # Test : `bash plot-cwls.sh "../../" "run.cwl" "runs-wfls.txt" "runs"`
        arcRoot=$1 arcRoot=$1
        cwlPattern=$2 cwlPattern=$2
        outWflList=$3 outWflList=$3
        ...@@ -8,8 +12,6 @@ find "$arcRoot"/ -name "$cwlPattern" > "$outWflList" ...@@ -8,8 +12,6 @@ find "$arcRoot"/ -name "$cwlPattern" > "$outWflList"
        mkdir -p "$outGraphs" mkdir -p "$outGraphs"
        while IFS= read -r wfl; do while IFS= read -r wfl; do
        dirname "$wfl" | xargs basename | xargs read wflname read wflname < <(dirname "$wfl" | xargs basename)
        cwltool --print-dot "$wfl" | dot -Tsvg > "$outGraphs"/"$wflname".svg cwltool --print-dot "$wfl" | dot -Tsvg > "$outGraphs"/"$wflname".svg
        done < "$outWflList" done < "$outWflList"
        \ No newline at end of file
        .cwl/cwl-plots/validate-workflows.yml → .cwl/cwl-plots/plot-workflows.yml
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        ...@@ -3,4 +3,4 @@ arcRoot: ...@@ -3,4 +3,4 @@ arcRoot:
        path: "../../" path: "../../"
        cwlPattern: "workflow.cwl" cwlPattern: "workflow.cwl"
        outWflList: "workflow-wfls.txt" outWflList: "workflow-wfls.txt"
        outValidation: "validate-workflows.txt" outGraphs: "workflows"
        \ No newline at end of file \ No newline at end of file
        .cwl/cwl-plots/plot.cwl
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        #!/usr/bin/env cwl-runner #!/usr/bin/env cwl-runner
        cwlVersion: v1.2 cwlVersion: v1.2
        class: CommandLineTool class: Workflow
        requirements:
        InitialWorkDirRequirement:
        listing:
        - entryname: plot-cwls.sh
        entry:
        $include: plot-cwls.sh
        baseCommand: ["bash", "plot-cwls.sh"]
        inputs: inputs:
        arcRoot: arcRoot:
        type: Directory type: Directory
        inputBinding: cwlPattern:
        position: 1 type: string
        cwlPattern: outWflList:
        type: string type: string
        inputBinding: outGraphs:
        position: 2 type: string
        outWflList:
        type: string
        inputBinding:
        position: 3
        outGraphs:
        type: string
        inputBinding:
        position: 4
        outputs: outputs:
        output_files: outputDir:
        type: File[] type: Directory
        outputBinding: outputSource: collect_files/outDir
        glob: $(inputs.outGraphs)/*.svg
        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]
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        </g>
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        </g>
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        .cwl/cwl-plots/runs/isaSampleToRawDataSeq.svg 0 → 100644
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        # Facultative CAM in Talinum # Facultative CAM in Talinum
        ## Data origin This ARC is based on Brilhaus et al. (2016). <https://doi.org/10.1104/pp.15.01076>. See [isa.investigation.xlsx](./isa.investigation.xlsx) for details.
        The [Talinum Genome Draft](./studies/TalinumGenomeDraft) originates from <https://git.nfdi4plants.org/hhu-plant-biochemistry/talinum-fruticosum-genome>
        - see [isa.investigation.xlsx](./isa.investigation.xlsx) for details
        - Adapted from
        > Brilhaus, D., Bräutigam, A., Mettler-Altmann, T., Winter, K., and Weber, A.P.M. (2016). Reversible Burst of Transcriptional Changes during Induction of Crassulacean Acid Metabolism in *Talinum triangulare*. Plant Physiology 170: 102–122. <https://doi.org/10.1104/pp.15.01076>
        - [studies/TalinumGenomeDraft](./studies/TalinumGenomeDraft) originates from <https://git.nfdi4plants.org/hhu-plant-biochemistry/talinum-fruticosum-genome>
        <!--- Start of automated section -->
        # Facultative CAM in Talinum triangulare
        ## Table of Contents ## Table of Contents
        1. [Description](#description) 1. [Description](#description)
        1. [Contacts](#contacts)
        2. [Publication](#publication) 2. [Publication](#publication)
        3. Studies 3. Studies
        - [TalinumGenomeDraft](#study--talinumgenomedraft) - [TalinumGenomeDraft](#study--talinumgenomedraft)
        ...@@ -87,16 +78,6 @@ class TalinumGenomeDraft,plant_material,mh-quant-results,mh-quant-report,rna_ext ...@@ -87,16 +78,6 @@ class TalinumGenomeDraft,plant_material,mh-quant-results,mh-quant-report,rna_ext
        | Assay identifiers | MassHunter_targets , Talinum_RNASeq_minimal , GCqTOF_targets | | Assay identifiers | MassHunter_targets , Talinum_RNASeq_minimal , GCqTOF_targets |
        | Assay Count | 3 | | Assay Count | 3 |
        ## Contacts
        | Names | Email | Address | Affiliation | ORCID |
        | ----- | ----- | ------- | ----------- | ----- |
        | Dominik Brilhaus | <brilhaus@hhu.de> | HHU Düsseldorf, 22.07.U1.43, Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | <http://orcid.org/0000-0001-9021-3197> |
        | Andrea Bräutigam | <andrea.brauetigam@hhu.de> | Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | <http://orcid.org/0000-0002-5309-0527> |
        | Tabea Mettler-Altmann | <tabea.mettler@hhu.de> | Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | <http://orcid.org/0000-0002-9161-4889> |
        | Klaus Winter | <winterk@si.edu> | Balboa, Ancón, Republic of Panama | Smithsonian Tropical Research Institute, Panama | |
        | Andreas P M Weber | <aweber@hhu.de> | Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | <http://orcid.org/0000-0003-0970-4672> |
        ## Publication ## Publication
        | Meta Data | Description | | Meta Data | Description |
        ...@@ -191,5 +172,3 @@ class TalinumGenomeDraft,plant_material,mh-quant-results,mh-quant-report,rna_ext ...@@ -191,5 +172,3 @@ class TalinumGenomeDraft,plant_material,mh-quant-results,mh-quant-report,rna_ext
        ### Annotation headers ### Annotation headers
        **Parameters**: [Bio entity](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000012),[Biosource amount](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000013),[Biosource material state](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010009),[Extraction buffer](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000050),[Extraction buffer volume](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000051),[Internal standard](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010012),[Sample volume](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010013),[MS sample post-extraction](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000043),[MS sample resuspension](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000044),[MS derivatization](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000052),[MS sample type](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000045),[Chromatography instrument model](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000046),[Chromatography autosampler model](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000047),[Chromatography column type](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000053),[Chromatography column model](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000048),[mobile phase](http://purl.obolibrary.org/obo/CHMO_0000995),[Chromatography injection volume](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010014),[Chromatography injection mode](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010015),[Chromatography gradient](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000081),[scan polarity](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000465),[scan window lower limit](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000501),[scan window upper limit](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000500),[scan rate](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000015),[instrument model](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000031),[ionization type](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000008),[mass analyzer type](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000443),[detector type](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000026) **Parameters**: [Bio entity](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000012),[Biosource amount](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000013),[Biosource material state](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010009),[Extraction buffer](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000050),[Extraction buffer volume](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000051),[Internal standard](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010012),[Sample volume](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010013),[MS sample post-extraction](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000043),[MS sample resuspension](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000044),[MS derivatization](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000052),[MS sample type](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000045),[Chromatography instrument model](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000046),[Chromatography autosampler model](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000047),[Chromatography column type](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000053),[Chromatography column model](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000048),[mobile phase](http://purl.obolibrary.org/obo/CHMO_0000995),[Chromatography injection volume](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010014),[Chromatography injection mode](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010015),[Chromatography gradient](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000081),[scan polarity](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000465),[scan window lower limit](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000501),[scan window upper limit](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000500),[scan rate](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000015),[instrument model](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000031),[ionization type](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000008),[mass analyzer type](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000443),[detector type](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000026)
        <!--- End of automated section -->
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        # Runs
        See [.cwl/README.md](../.cwl/README.md) for more info.
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