Workflow: bam to trimmed fastqs and HISAT alignments
Fetched 2023-01-12 05:05:23 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 |
|---|---|---|---|
| bam | File | ||
| adapters | File | ||
| firststrand | Boolean (Optional) | ||
| max_uncalled | Integer | ||
| secondstrand | 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 |
trim_fastq.cwl
(CommandLineTool)
|
Trim FASTQ (flexbar) | |
| bam_to_fastq |
bam_to_fastq.cwl
(CommandLineTool)
|
Picard: BAM to FASTQ | |
| hisat2_align |
hisat2_align.cwl
(CommandLineTool)
|
HISAT2: align |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| fastqs | File[] | ||
| aligned_bam | File |
Permalink:
https://w3id.org/cwl/view/git/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/rnaseq/bam_to_trimmed_fastq_and_hisat_alignments.cwl
