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class: Workflow
cwlVersion: v1.0
id: cpo_pipeline
label: cpo-pipeline
$namespaces:
edam: "http://edamontology.org/"
s: https://schema.org/
$schemas:
- "http://edamontology.org/EDAM_1.16.owl"
inputs:
- id: reads2
type: File
format: 'edam:format_1932'
- id: reads1
type: File
format: 'edam:format_1932'
- id: refseq_genomes_k21_s1000_msh
type: File
outputs:
- id: mlst_output
outputSource: "mlst/output"
type: File
- id: fastqc_R1_output
outputSource: "fastqc_reads1/output"
type: Directory
- id: fastqc_R2_output
outputSource: "fastqc_reads2/output"
type: Directory
- id: quast_output
outputSource: "quast/output"
type: Directory
- id: mash_dist_output
outputSource: "head/output"
type: File
steps:
- id: shovill
in:
- id: reads1
source: reads1
- id: reads2
source: reads2
out:
- id: contigs
- id: contig-graph
- id: log
run: https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/shovill/shovill.cwl
label: shovill
- id: mlst
in:
- id: input
source: shovill/contigs
out:
- id: output
run: https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/mlst/mlst.cwl
label: mlst
- id: quast
in:
- id: contigs
source:
- shovill/contigs
out:
- id: output
run: https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/quast/quast.cwl
label: quast
- id: mash_dist
in:
- id: reference
source: refseq_genomes_k21_s1000_msh
- id: query
source:
- mash_sketch/output
out:
- id: output
run: https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/mash/mash_dist/mash_dist.cwl
label: mash_dist
- id: mash_sketch
in:
- id: R1
source: reads1
- id: R2
source: reads2
out:
- id: output
run: https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/mash/mash_sketch/mash_sketch.cwl
label: mash_sketch
- id: sort
in:
- id: input
source: mash_dist/output
- id: keydef
default: '2,2'
- id: general-numeric-sort
default: true
out:
- id: output
run: https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/sort/sort.cwl
label: sort
- id: fastqc_reads1
in:
- id: input
source:
- reads1
out:
- id: output
run: https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/fastqc/fastqc.cwl
label: fastqc
- id: fastqc_reads2
in:
- id: input
source:
- reads2
out:
- id: output
run: https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/fastqc/fastqc.cwl
label: fastqc
- id: head
in:
- id: count
default: 1
- id: input
source: sort/output
out:
- id: output
run: https://raw.githubusercontent.com/dfornika/cwl-workspace/master/tools/head/head.cwl
label: head
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