Workflow: workflow_mock_ngtax.cwl

Fetched 2023-01-08 15:19:18 GMT
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Inputs

ID Type Title Doc
mock3 String (Optional) Mock3 reference

Mock3 reference selection
mock4 String (Optional) Mock4 reference

Mock4 reference selection
sample String Sample name

Name of the sample being analysed
fragment String Subfragment name

Subfragment that is being analysed (e.g. V1-V3 or V5-region)
metadata File (Optional) Metadata file

UNLOCK assay metadata file
destination String (Optional) Output Destination

Optional Output destination used for cwl-prov reporting.
for_read_len Integer Reverse read length

Read length of the reverse read
reference_db String (Optional) Reference database

Reference database used in FASTA format
rev_read_len Integer (Optional) Reverse read length

Read length of the reverse read
forward_primer String Forward primer

Forward primer used
reverse_primer String (Optional) Reverse primer

Reverse primer used

Steps

ID Runs Label Doc
ngtax
../ngtax/ngtax.cwl (CommandLineTool)
NGTax amplicon analysis

Runs NGTAX amplicon analysis

ngtax_to_tsv-fasta
../ngtax/ngtax_to_tsv-fasta.cwl (CommandLineTool)

NGtax2 output conversion to prepare for biom file and ASV fasta file

ngtax_files_to_folder
../expressions/files_to_folder.cwl (ExpressionTool)

Transforms the input files to a mentioned directory

phyloseq_files_to_folder
../expressions/files_to_folder.cwl (ExpressionTool)

Transforms the input files to a mentioned directory

Outputs

ID Type Label Doc
files_to_folder_ngtax Directory
files_to_folder_phyloseq Directory
html json turtle jsonld rdfxml svg png dot zip ro yaml raw
Permalink: https://w3id.org/cwl/view/git/60fafdfbec9b39c860945ef4634e0c28cb5e976c/cwl/workflows/workflow_mock_ngtax.cwl