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workflow.cwl
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workflow.cwl
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#!usr/bin/env cwl-runner
cwlVersion: v1.2
class: Workflow
requirements:
InlineJavascriptRequirement: {}
ScatterFeatureRequirement: {}
MultipleInputFeatureRequirement: {}
SubworkflowFeatureRequirement: {}
inputs:
fastq_directory: Directory
db_path:
type:
- Directory
- File
secondaryFiles:
- $("opts.k2d")
- $("taxo.k2d")
threads: int?
index:
type: File
secondaryFiles:
- .amb
- .ann
- .bwt
- .fai
- .pac
- .sa
outputs:
unmapped_R1:
type: File[]
outputSource: humanmapper/unmapped_R1
unmapped_R2:
type: File[]
outputSource: humanmapper/unmapped_R2
kraken2_output:
type: File[]
outputSource: kraken2/kraken2
kraken2_report:
type: File[]
outputSource: kraken2/report
kraken-biom_output:
type: File
outputSource: kraken-biom/biom
get-otu_output:
type: File[]
outputSource: get-otu/otu_table
count-total-otu_output:
type: File
outputSource: count-total-otu/total_otu
compute-alpha_output:
type: File
outputSource: compute-alpha/alpha_div
steps:
check-input:
run: cwl/checkInput.cwl
in:
fastq_directory: fastq_directory
out: [read_1, read_2]
humanmapper:
run: cwl/humanMapper.cwl
scatter: [read_1, read_2]
scatterMethod: dotproduct
in:
read_1: check-input/read_1
read_2: check-input/read_2
index: index
threads: threads
out: [unmapped_R1, unmapped_R2]
kraken2:
run: cwl/kraken2.cwl
scatter: [read_1, read_2]
scatterMethod: dotproduct
in:
read_1: humanmapper/unmapped_R1
read_2: humanmapper/unmapped_R2
db_path: db_path
threads: threads
out: [kraken2, report]
kraken-biom:
run: cwl/kraken-biom.cwl
in:
kraken_report: kraken2/report
out: [biom]
get-otu:
run: cwl/getOTU.cwl
scatter: kraken_report
in:
kraken_report: kraken2/report
out: [otu_table]
count-total-otu:
run: cwl/countTotalOTU.cwl
in:
otus: get-otu/otu_table
out: [total_otu]
compute-alpha:
run: cwl/computeAlpha.cwl
in:
total_otu: count-total-otu/total_otu
out: [alpha_div]