Workflow: sequence (bam or fastqs) to trimmed fastqs and HISAT alignments
Fetched 2023-01-09 12:53:25 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| strand | |||
| adapters | File | ||
| unaligned | https://w3id.org/cwl/view/git/fbeea265295ae596d5a3ba563e766be0c4fc26e8/definitions/types/sequence_data.yml#sequence_data | ||
| max_uncalled | Integer | ||
| unzip_fastqs | Boolean (Optional) | ||
| read_group_id | String | ||
| min_readlength | Integer | ||
| reference_index | File | ||
| adapter_trim_end | String | ||
| read_group_fields | String[] | ||
| adapter_min_overlap | Integer |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| trim_fastq |
../tools/trim_fastq.cwl
(CommandLineTool)
|
Trim FASTQ (flexbar) | |
| hisat2_align |
../tools/hisat2_align.cwl
(CommandLineTool)
|
HISAT2: align | |
| sequence_to_fastq |
../tools/sequence_to_fastq.cwl
(CommandLineTool)
|
Picard: BAM to FASTQ |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| fastqs | File[] | ||
| aligned_bam | File |
Permalink:
https://w3id.org/cwl/view/git/fbeea265295ae596d5a3ba563e766be0c4fc26e8/definitions/subworkflows/sequence_to_trimmed_fastq_and_hisat_alignments.cwl
