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Commit 943e5e52 authored by Dominik Brilhaus's avatar Dominik Brilhaus
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switch kallisto input to array of records

parent c67b71f2
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1 merge request!14Cwl
Pipeline #9385 failed
Stage: arc_json
    Stage: quality_report_generator
      Stage: quality_report
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        runs/kallisto/run.cwl
        + 11
        − 8
        View file @ 943e5e52
        ...@@ -4,16 +4,20 @@ class: Workflow ...@@ -4,16 +4,20 @@ class: Workflow
        requirements: requirements:
        SubworkflowFeatureRequirement: {} SubworkflowFeatureRequirement: {}
        MultipleInputFeatureRequirement: {}
        inputs: inputs:
        IndexInput: File[] IndexInput: File[]
        InputReadsMultipleSamples: sampleRecord:
        type: type:
        type: array type: array
        items: items:
        type: array type: record
        items: File fields:
        numUnderscoresFileName: int readsOfOneSample:
        type: File[]
        sampleName:
        type: string?
        isSingle: boolean isSingle: boolean
        FragmentLength: double? FragmentLength: double?
        StandardDeviation: double? StandardDeviation: double?
        ...@@ -25,8 +29,7 @@ steps: ...@@ -25,8 +29,7 @@ steps:
        run: ../../workflows/kallisto/workflow.cwl run: ../../workflows/kallisto/workflow.cwl
        in: in:
        IndexInput: IndexInput IndexInput: IndexInput
        InputReadsMultipleSamples: InputReadsMultipleSamples sampleRecord: sampleRecord
        numUnderscoresFileName: numUnderscoresFileName
        isSingle: isSingle isSingle: isSingle
        FragmentLength: FragmentLength FragmentLength: FragmentLength
        StandardDeviation: StandardDeviation StandardDeviation: StandardDeviation
        ......
        runs/kallisto/run.yml
        + 30
        − 27
        View file @ 943e5e52
        ...@@ -5,44 +5,47 @@ IndexInput: ...@@ -5,44 +5,47 @@ IndexInput:
        format: edam:format_1929 # FASTA format: edam:format_1929 # FASTA
        ## Fastq files to be mapped ## Fastq files to be mapped
        # The `InputReadsMultipleSamples` looks more complicated than needed # The `readsOfOneSample` looks more complicated than needed
        # It's an array of File arrays to generically allow multiple fastq files per sample # It's an array of records (each with one or mupltiple files and a sample name) to generically allow multiple fastq files per sample
        InputReadsMultipleSamples: sampleRecord:
        - - readsOfOneSample:
        - class: File - class: File
        path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
        format: edam:format_1930 # FASTQ format: edam:format_1930
        - sampleName: 'DB_097'
        - readsOfOneSample:
        - class: File
        path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
        format: edam:format_1930
        sampleName: 'DB_163'
        - readsOfOneSample:
        - class: File - class: File
        path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
        format: edam:format_1930 # FASTQ format: edam:format_1930
        # - sampleName: 'DB_099'
        # - class: File - readsOfOneSample:
        # path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz - class: File
        # format: edam:format_1930 # FASTQ path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
        # - format: edam:format_1930
        # - class: File sampleName: 'DB_103'
        # path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz - readsOfOneSample:
        # format: edam:format_1930 # FASTQ - class: File
        # - path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
        # - class: File format: edam:format_1930
        # path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz sampleName: 'DB_161'
        # format: edam:format_1930 # FASTQ - readsOfOneSample:
        # - - class: File
        # - class: File path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
        # path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz format: edam:format_1930
        # format: edam:format_1930 # FASTQ sampleName: 'DB_165'
        numUnderscoresFileName: 2
        ### Kallisto quant Parameters ### Kallisto quant Parameters
        isSingle: true isSingle: true
        FragmentLength: 200 FragmentLength: 200
        StandardDeviation: 20 StandardDeviation: 20
        BootstrapSamples: 30 BootstrapSamples: 30
        resultsFolder: kallisto_results
        resultsFolder: test
        $namespaces: $namespaces:
        edam: https://edamontology.org/ edam: https://edamontology.org/
        \ No newline at end of file
        workflows/kallisto/workflow.cwl
        + 51
        − 48
        View file @ 943e5e52
        #!/usr/bin/env cwl-runner
        cwlVersion: v1.2 cwlVersion: v1.2
        class: Workflow class: Workflow
        ...@@ -7,56 +8,58 @@ requirements: ...@@ -7,56 +8,58 @@ requirements:
        InlineJavascriptRequirement: {} InlineJavascriptRequirement: {}
        inputs: inputs:
        IndexInput: File[] IndexInput: File[]
        sampleRecord: sampleRecord:
        type: type:
        type: array type: array
        items: items:
        type: record type: record
        fields: fields:
        readsOfOneSample: readsOfOneSample:
        type: File[] type: File[]
        sampleName: sampleName:
        type: string? type: string?
        isSingle: boolean isSingle: boolean
        FragmentLength: double? FragmentLength: double?
        StandardDeviation: double? StandardDeviation: double?
        BootstrapSamples: int? BootstrapSamples: int?
        resultsFolder: string resultsFolder: string
        steps: steps:
        index: index:
        run: kallisto-index.cwl run: kallisto-index.cwl
        in: in:
        InputFiles: IndexInput InputFiles: IndexInput
        IndexName: IndexName:
        source: IndexInput source: IndexInput
        valueFrom: $(self[0].nameroot) valueFrom: $(self[0].nameroot)
        out: [index] out: [index]
        quant:
        run: kallisto-quant.cwl quant:
        scatter: [InputReads, QuantOutfolder] run: kallisto-quant.cwl
        scatterMethod: dotproduct scatter: [InputReads, QuantOutfolder]
        in: scatterMethod: dotproduct
        InputReads: in:
        source: sampleRecord InputReads:
        valueFrom: $(self.readsOfOneSample) source: sampleRecord
        QuantOutfolder: valueFrom: $(self.readsOfOneSample)
        source: sampleRecord QuantOutfolder:
        valueFrom: $(self.sampleName) source: sampleRecord
        Index: index/index valueFrom: $(self.sampleName)
        isSingle: isSingle Index: index/index
        FragmentLength: FragmentLength isSingle: isSingle
        StandardDeviation: StandardDeviation FragmentLength: FragmentLength
        BootstrapSamples: BootstrapSamples StandardDeviation: StandardDeviation
        out: [outFolder] BootstrapSamples: BootstrapSamples
        collectResults: out: [outFolder]
        run: ./yield-dirInDestination.cwl
        scatter: inDir collectResults:
        in: run: ./yield-dirInDestination.cwl
        inDir: quant/outFolder scatter: inDir
        destinationDir: resultsFolder in:
        out: [outDir] inDir: quant/outFolder
        destinationDir: resultsFolder
        out: [outDir]
        outputs: outputs:
        finalOut: finalOut:
        ......
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