Workflow: assembly-1.cwl
Fetched 2026-01-16 03:51:34 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| contigs | File | ||
| contig_min_length | Integer |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| unzip |
/cwl/view/git/49ae257c560e71d2946290d1705b2912fd81f76f/utils/multiple-gunzip.cwl
(CommandLineTool)
|
unzip files | |
| QC-FLAG |
/cwl/view/git/49ae257c560e71d2946290d1705b2912fd81f76f/utils/qc-flag.cwl
(CommandLineTool)
|
output QC-FAILED or QC-PASSED file as intermediate flag | |
| hashsum |
/cwl/view/git/49ae257c560e71d2946290d1705b2912fd81f76f/utils/generate_checksum/generate_checksum.cwl
(CommandLineTool)
|
||
| qc_stats |
/cwl/view/git/49ae257c560e71d2946290d1705b2912fd81f76f/tools/qc-stats/qc-stats.cwl
(CommandLineTool)
|
Post QC-ed input analysis of sequence file | |
| count_reads |
/cwl/view/git/49ae257c560e71d2946290d1705b2912fd81f76f/utils/count_fasta.cwl
(CommandLineTool)
|
||
| clean_headers |
/cwl/view/git/49ae257c560e71d2946290d1705b2912fd81f76f/utils/clean_fasta_headers.cwl
(CommandLineTool)
|
Replaces problematic characters from FASTA headers with dashes | |
| length_filter |
/cwl/view/git/49ae257c560e71d2946290d1705b2912fd81f76f/tools/qc-filtering/qc-filtering.cwl
(CommandLineTool)
|
Quality control filtering step using the BioPython package. | |
| count_processed_reads |
/cwl/view/git/49ae257c560e71d2946290d1705b2912fd81f76f/utils/count_fasta.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| qc-status | File | ||
| qc_summary | File | ||
| hashsum_input | File | ||
| filtered_fasta | File | ||
| qc-statistics_folder | Directory |
Permalink:
https://w3id.org/cwl/view/git/49ae257c560e71d2946290d1705b2912fd81f76f/workflows/conditionals/assembly/assembly-1.cwl
