diff --git a/.gitignore b/.gitignore index 11819f2d595ad57d5666a7dea2cb52f9fe976118..bce78f50b1178bcfbc525e32d354f9e41d55edef 100644 --- a/.gitignore +++ b/.gitignore @@ -386,3 +386,6 @@ Temporary Items # R temporaries .Rhistory .RData + +# CWL caches +**/cache*/ \ No newline at end of file diff --git a/runs/kallisto/README.md b/runs/kallisto/README.md index 65d21cd4f3ce6e4d1656367abbdf063c3302894e..2f01d0737e9a9013e5c7b90cad4996e978a603ea 100644 --- a/runs/kallisto/README.md +++ b/runs/kallisto/README.md @@ -6,4 +6,3 @@ cd runs/kallisto/ cwltool --cachedir cache2 ../../workflows/kallisto/kallisto-workflow.cwl workflow.yml > $(date +"%Y-%m-%d_%H-%M").log 2>&1 & ``` - diff --git a/runs/kallisto/workflow.yml b/runs/kallisto/workflow.yml index e1d32d5b1c395e3aceb975b84d7bc2489a7e74e8..db33ad666d253942c4ab8a07f96284b38839fcf4 100644 --- a/runs/kallisto/workflow.yml +++ b/runs/kallisto/workflow.yml @@ -1,4 +1,14 @@ -InputReadsMultipleSamples: +## Genome file to build kallisto Index +IndexInput: + - class: File + path: ../../studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa + format: edam:format_1929 # FASTA + +## Fastq files to be mapped +# The `InputReadsMultipleSamples` looks more complicated than needed +# It's an array of File arrays to generically allow multiple fastq files per sample + +InputReadsMultipleSamples: - - class: File path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz @@ -7,14 +17,13 @@ InputReadsMultipleSamples: - class: File path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz format: edam:format_1930 # FASTQ -IndexInput: - - class: File - path: ../../studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa - format: edam:format_1929 # FASTA + +numCharsFastqFileName: 6 +### Kallisto quant Parameters isSingle: true FragmentLength: 200 StandardDeviation: 20 -BootstrapSamples: 30 +BootstrapSamples: 1 $namespaces: edam: https://edamontology.org/ \ No newline at end of file diff --git a/workflows/kallisto/kallisto-quant.cwl b/workflows/kallisto/kallisto-quant.cwl index 8267499b916ae168a2f9e2d3927de99fea6715a9..9d6df5f0d6dd8502cecb916830c25685d3e791db 100755 --- a/workflows/kallisto/kallisto-quant.cwl +++ b/workflows/kallisto/kallisto-quant.cwl @@ -132,6 +132,6 @@ outputs: glob: $(runtime.outdir)/$(inputs.QuantOutfolder) $namespaces: - edam: http://edamontology.org/ + edam: https://edamontology.org/ $schemas: - https://edamontology.org/EDAM_1.18.owl diff --git a/workflows/kallisto/kallisto-workflow.cwl b/workflows/kallisto/kallisto-workflow.cwl index 37fb7dfc8908349e5b37ded7e973efd1841f3625..c0e074e8d8c1cdf6f5187ea90c4cb9a12373beb9 100644 --- a/workflows/kallisto/kallisto-workflow.cwl +++ b/workflows/kallisto/kallisto-workflow.cwl @@ -7,13 +7,14 @@ requirements: InlineJavascriptRequirement: {} inputs: + IndexInput: File[] InputReadsMultipleSamples: type: type: array items: type: array items: File - IndexInput: File[] + numCharsFastqFileName: int? isSingle: boolean FragmentLength: double? StandardDeviation: double? @@ -30,13 +31,15 @@ steps: out: [index] quant: run: kallisto-quant.cwl - scatter: InputReads + scatter: + - InputReads + - QuantOutfolder + scatterMethod: dotproduct in: InputReads: InputReadsMultipleSamples QuantOutfolder: - # source: InputReadsMultipleSamples - # valueFrom: $(self[0].nameroot) - valueFrom: testSample + source: InputReadsMultipleSamples + valueFrom: $(self[0].nameroot) Index: index/index isSingle: isSingle FragmentLength: FragmentLength