Commit 0f9e111a authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

obsolete

parent 934bf3f2
#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: Workflow
requirements:
StepInputExpressionRequirement: {}
InlineJavascriptRequirement: {}
MultipleInputFeatureRequirement: {}
SubworkflowFeatureRequirement: {}
ScatterFeatureRequirement: {}
label: Metagenomics workflow
doc: |
Workflow for Metagenomics from bins to annotated bins.
Steps:
- MetaBat2 (binning) input
- SAPP
- Conversion to RDF
- Prodigal gene prediction
- InterProScan annotation
outputs:
sapp_output:
label: SAPP Genomes
type: Directory
doc: Folder containing genomes annotated by SAPP
outputSource: sapp_files_to_folder/results
inputs:
fasta:
type: File[]
doc: List of binned fasta files
label: bin .fa files
threads:
type: int?
doc: number of threads to use for computational processes
label: number of threads
default: 4
steps:
#########################################
# bin annotation using SAPP
workflow_sapp:
doc: Semantic Annotation Platform with Provenance to annotate each bin obtained from metabat2
label: Semantic Annotation Platform with Provenance
run: workflow_sapp_microbes.cwl
scatter: [fasta]
in:
fasta: fasta
codon:
valueFrom: ${ return 11; }
identifier:
valueFrom: ${ return inputs.fasta.nameroot; }
single:
default: true
threads: threads
out: [conversion, prodigal, interproscan]
sapp_files_to_folder:
doc: Preparation of sapp output files to a specific output folder
label: SAPP output
run: ../expressions/files_to_folder.cwl
in:
files:
source: [workflow_sapp/conversion, workflow_sapp/prodigal , workflow_sapp/interproscan]
linkMerge: merge_flattened
destination:
valueFrom: $("8_SAPP")
out:
[results]
#############################################
s:author:
- class: s:Person
s:identifier: https://orcid.org/0000-0001-8172-8981
s:email: mailto:jasper.koehorst@wur.nl
s:name: Jasper Koehorst
- class: s:Person
s:identifier: https://orcid.org/0000-0001-9524-5964
s:email: mailto:bart.nijsse@wur.nl
s:name: Bart Nijsse
s:citation: https://m-unlock.nl
s:codeRepository: https://gitlab.com/m-unlock/cwl
s:dateCreated: "2020-00-00"
s:license: https://spdx.org/licenses/Apache-2.0
s:copyrightHolder: "UNLOCK - Unlocking Microbial Potential"
$namespaces:
s: https://schema.org/
\ No newline at end of file
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