Workflow: fastq_foreign_chromosome_cleanup
Fetched 2024-05-19 12:11:02 GMT
Verified with cwltool version 3.1.20230201224320
This workflow remove foreign chromosome comtamination from blastn TSV files
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/ncbi/cwl-ngs-workflows-cbb/master/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fastq1 | File | ||
| fastq2 | File (Optional) | ||
| threads | Integer | ||
| data_dir | Directory | ||
| tax_group | String | ||
| partitions | Integer | ||
| file_name_prefix | String | ||
| tax_group_pickle | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fastqc1 |
../../tools/fastqc/fastqc.cwl
(CommandLineTool)
|
FastQC |
BASH echo command |
| fastqc2 |
../../tools/fastqc/fastqc.cwl
(CommandLineTool)
|
FastQC |
BASH echo command |
| create_clean_fastq |
../../tools/bbmap/filterbyname.cwl
(CommandLineTool)
|
filterbyname |
Filterbyname |
| extract_clean_reads_ids |
../../tools/python/extract-clean-from-foreign-blastn.cwl
(CommandLineTool)
|
extract_foreign_contaminated_ids |
This tools remove contaminated reads from fastq using blastn results from Gtax TSV file |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| fastqc1_zip | File[] | ||
| fastqc2_zip | File[] (Optional) | ||
| fastqc1_html | File[] | ||
| fastqc2_html | File[] (Optional) | ||
| fastq1_output | File | ||
| fastq2_output | File (Optional) | ||
| decontaminated_reads_ids | File |
Permalink:
https://w3id.org/cwl/view/git/1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49/workflows/Contamination/fastq-foreign-chromosome-cleanup.cwl
