- 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/a83ee883bb3c7480010fa952939fac771491ddf4/utils/multiple-gunzip.cwl
(CommandLineTool)
|
unzip files | |
QC-FLAG |
/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/utils/qc-flag.cwl
(CommandLineTool)
|
output QC-FAILED or QC-PASSED file as intermediate flag | |
hashsum |
/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/utils/generate_checksum/generate_checksum.cwl
(CommandLineTool)
|
||
qc_stats |
/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/tools/qc-stats/qc-stats.cwl
(CommandLineTool)
|
Post QC-ed input analysis of sequence file | |
count_reads |
/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/utils/count_fasta.cwl
(CommandLineTool)
|
||
clean_headers |
/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/utils/clean_fasta_headers.cwl
(CommandLineTool)
|
Replaces problematic characters from FASTA headers with dashes | |
length_filter |
/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/tools/qc-filtering/qc-filtering.cwl
(CommandLineTool)
|
Quality control filtering step using the BioPython package. | |
count_processed_reads |
/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/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/a83ee883bb3c7480010fa952939fac771491ddf4/workflows/conditionals/assembly/assembly-1.cwl