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16S_taxonomic_analysis.cwl
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16S_taxonomic_analysis.cwl
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cwlVersion: v1.0
class: Workflow
label: Functional analyis of sequences that match the 16S SSU
requirements:
- class: SchemaDefRequirement
types:
- $import: ../tools/biom-convert-table.yaml
inputs:
16S_matches:
type: File
outputs:
otu_table_summary:
type: File
outputSource: create_otu_text_summary/otu_table_summary
tree:
type: File
outputSource: prune_tree/pruned_tree
biom_tsv:
type: File
outputSource: convert_new_biom_to_classic/result
biom_json:
type: File
outputSource: convert_new_biom_to_old_biom/result
biom_hdf5:
type: File
outputSource: convert_otu_counts_to_hdf5/result
qiime_sequences-filtered_clusters:
type: File
outputSource: pick_closed_reference_otus/sequences-filtered_clusters
qiime_sequences-filtered_otus:
type: File
outputSource: pick_closed_reference_otus/sequences-filtered_otus
qiime_assigned_taxonomy:
type: File
outputSource: modify_taxonomy_table/qiime_assigned_taxonomy
steps:
pick_closed_reference_otus:
run: ../tools/qiime-pick_closed_reference_otus.cwl
in:
sequences: 16S_matches
out:
- otu_table
- otus_tree
- sequences-filtered_clusters
- sequences-filtered_otus
- sequences-filtered_otus_log
modify_taxonomy_table:
run: ../tools/modify_taxonomy_table.cwl
in:
uclust_log: pick_closed_reference_otus/sequences-filtered_otus_log
otu_table: convert_new_biom_to_classic/result
out: [ qiime_assigned_taxonomy ]
convert_new_biom_to_old_biom:
run: ../tools/biom-convert.cwl
in:
biom: pick_closed_reference_otus/otu_table
table_type: { default: OTU table }
json: { default: true }
out: [ result ]
convert_new_biom_to_classic:
run: ../tools/biom-convert.cwl
in:
biom: pick_closed_reference_otus/otu_table
header_key: { default: taxonomy }
table_type: { default: OTU table }
tsv: { default: true }
out: [ result ]
convert_otu_counts_to_hdf5:
run: ../tools/biom-convert.cwl
in:
biom: pick_closed_reference_otus/otu_table
hdf5: { default: true }
table_type: { default: OTU table }
out: [ result ]
create_otu_text_summary:
run: ../tools/biom-summarize_table.cwl
in:
biom: pick_closed_reference_otus/otu_table
out: [ otu_table_summary ]
extract_observations:
run: ../tools/extract_observations.cwl
in:
tsv_otu_table: convert_new_biom_to_classic/result
out: [ observations ]
prune_tree:
run: ../tools/qiime-filter_tree.cwl
in:
tree: pick_closed_reference_otus/otus_tree
tips_or_seqids_to_retain: extract_observations/observations
out: [ pruned_tree ]
$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"