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Commit bc4095f4 authored by Dominik Brilhaus's avatar Dominik Brilhaus
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Merge branch 'arc-cwl' into 'main' 

Arc cwl

See merge request !19
parents 0bf412a4 73782263
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1 merge request!19Arc cwl
Pipeline #9529 passed
Stage: arc_json
    Stage: quality_report_generator
      Stage: quality_report
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        .cwl/README.md
        + 1
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        View file @ bc4095f4
        ......@@ -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
        ```
        .cwl/arc-cwl.svg 0 → 100644
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        View file @ bc4095f4
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        View file @ bc4095f4
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        ......
        README.md
        + 29
        − 10
        View file @ bc4095f4
        ......@@ -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
        ![arc.cwl](.cwl/arc-cwl.svg)
        ## Additional details
        | Meta Data | Description |
        | --------- | ----------- |
        ......
        arc-job.yml 0 → 100644
        + 76
        − 0
        View file @ bc4095f4
        ################################################################################
        ### 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
        arc.cwl 0 → 100644
        + 80
        − 0
        View file @ bc4095f4
        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
        runs/fastqc/run.cwl
        + 3
        − 3
        View file @ bc4095f4
        ......@@ -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
        runs/isaSampleToRawDataSeq/rnaseq-samples.xlsx
        + 0
        − 0
        View file @ bc4095f4
        No preview for this file type
        runs/isaSampleToRawDataSeq/run.cwl
        + 9
        − 5
        View file @ bc4095f4
        ......@@ -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
        runs/kallisto/run.cwl
        + 4
        − 4
        View file @ bc4095f4
        ......@@ -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
        runs/sleuth/run.cwl
        + 2
        − 2
        View file @ bc4095f4
        ......@@ -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
        workflows/fastqc/fastqc.cwl
        + 19
        − 5
        View file @ bc4095f4
        ......@@ -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
        workflows/fastqc/collectFilesInDir.cwl → workflows/fastqc/gather-files.cwl
        + 24
        − 0
        View file @ bc4095f4
        cwlVersion: v1.2
        class: ExpressionTool
        label: Collect files in a directory
        label: Gather files
        doc: |
        Takes Files (e.g. from a workflow step) and yields them in a desired directory.
        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:
        files: File[]
        inFiles: File[]
        destination: string
        expression: |
        ${
        return {"outDir": {
        "class": "Directory",
        "basename": inputs.destination,
        "listing": inputs.files
        "listing": inputs.inFiles
        } };
        }
        outputs:
        ......
        workflows/fastqc/workflow.cwl
        + 7
        − 5
        View file @ bc4095f4
        ......@@ -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
        workflows/isaSampleToRawDataSeq/workflow.cwl
        + 6
        − 2
        View file @ bc4095f4
        ......@@ -39,9 +39,13 @@ inputs:
        position: 4
        outputs:
        output:
        type: File[]
        sampleseqCsv:
        type: File
        outputBinding:
        glob:
        - "*.csv"
        sampleseqXlsx:
        type: File
        outputBinding:
        glob:
        - "*.xlsx"
        workflows/kallisto/yield-dirInDestination.cwl → workflows/kallisto/gather-dirs.cwl
        + 28
        − 0
        View file @ bc4095f4
        cwlVersion: v1.2
        class: ExpressionTool
        label: Gather directories
        doc: |
        Takes a directory (e.g. from a workflow step) and yields it in a desired directory.
        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:
        inDir: Directory
        inDirs: Directory[]
        destinationDir: string
        expression: |
        ${
        return {"outDir": {
        "class": "Directory",
        "basename": inputs.destinationDir,
        "listing": [inputs.inDir]
        "listing": inputs.inDirs
        } };
        }
        outputs:
        outDir: Directory
        \ No newline at end of file
        workflows/kallisto/kallisto-index.cwl
        + 36
        − 5
        View file @ bc4095f4
        ......@@ -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
        workflows/kallisto/kallisto-quant.cwl
        + 44
        − 2
        View file @ bc4095f4
        ......@@ -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
        workflows/kallisto/kallisto-test.cwl deleted 100644 → 0
        + 0
        − 18
        View file @ 0bf412a4
        #!/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
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