Workflow: Quality assessment, amplicon classification
Fetched 2024-07-16 22:32:44 GMT
Verified with cwltool version 3.1.20221201130942
Workflow for quality assessment of paired reads and classification using NGTax 2.0. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Export module
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| 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_reads | File | forward reads |
forward sequence file locally |
| reverse_reads | File (Optional) | reverse reads |
reverse sequence file locally |
| forward_primer | String | Forward primer |
Forward primer used |
| primersRemoved | Boolean (Optional) | Primers are removed |
Wether the primers are removed or not from the input files |
| 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 |
| fastqc |
../fastqc/fastqc.cwl
(CommandLineTool)
|
FASTQC |
Performs quality control on FASTQ files |
| reads_to_folder |
../expressions/files_to_folder.cwl
(ExpressionTool)
|
Transforms the input files to a mentioned directory |
|
| 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 |
|
| fastqc_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 |
|---|---|---|---|
| turtle | File |
Used for other workflows |
|
| files_to_folder_ngtax | Directory | ||
| files_to_folder_fastqc | Directory | ||
| files_to_folder_phyloseq | Directory |
https://w3id.org/cwl/view/git/b9097b82e6ab6f2c9496013ce4dd6877092956a0/cwl/workflows/workflow_ngtax.cwl
