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emg-pipeline-v3-paired.cwl
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emg-pipeline-v3-paired.cwl
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cwlVersion: v1.0
class: Workflow
label: EMG pipeline v3.0 (paired end version)
requirements:
- class: SubworkflowFeatureRequirement
- class: SchemaDefRequirement
types:
- $import: ../tools/FragGeneScan-model.yaml
inputs:
forward_reads:
type: File
format: edam:format_1930 # FASTQ
reverse_reads:
type: File
format: edam:format_1930 # FASTQ
fraggenescan_model: ../tools/FragGeneScan-model.yaml#model
16S_model:
type: File
format: edam:format_1370 # HMMER
5S_model:
type: File
format: edam:format_1370 # HMMER
23S_model:
type: File
format: edam:format_1370 # HMMER
tRNA_model:
type: File
format: edam:format_1370 # HMMER
go_summary_config: File
outputs:
processed_sequences:
type: File
outputSource: unified_processing/processed_sequences
predicted_CDS:
type: File
outputSource: unified_processing/predicted_CDS
functional_annotations:
type: File
outputSource: unified_processing/functional_annotations
otu_table_summary:
type: File
outputSource: unified_processing/otu_table_summary
tree:
type: File
outputSource: unified_processing/tree
biom_json:
type: File
outputSource: unified_processing/biom_json
steps:
overlap_reads:
label: Paired-end overlapping reads are merged
run: ../tools/seqprep.cwl
in:
forward_reads: forward_reads
reverse_reads: reverse_reads
out: [ merged_reads, forward_unmerged_reads, reverse_unmerged_reads ]
combine_overlaped_and_unmerged_reads:
run: ../tools/seqprep-merge.cwl
in:
merged_reads: overlap_reads/merged_reads
forward_unmerged_reads: overlap_reads/forward_unmerged_reads
reverse_unmerged_reads: overlap_reads/reverse_unmerged_reads
out: [ merged_with_unmerged_reads ]
unified_processing:
label: continue with the main workflow
run: emg-pipeline-v3.cwl
in:
reads: combine_overlaped_and_unmerged_reads/merged_with_unmerged_reads
fraggenescan_model: fraggenescan_model
16S_model: 16S_model
5S_model: 5S_model
23S_model: 23S_model
tRNA_model: tRNA_model
go_summary_config: go_summary_config
out:
- processed_sequences
- predicted_CDS
- functional_annotations
- otu_table_summary
- tree
- biom_json
$namespaces:
edam: http://edamontology.org/
s: http://schema.org/
$schemas:
- http://edamontology.org/EDAM_1.16.owl
- https://schema.org/docs/schema_org_rdfa.html
s:license: "https://www.apache.org/licenses/LICENSE-2.0"
s:copyrightHolder: "EMBL - European Bioinformatics Institute"