- 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 | ||
strand | |||
adapters | File | ||
max_uncalled | Integer | ||
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) | |
bam_to_fastq |
../tools/bam_to_fastq.cwl
(CommandLineTool)
|
Picard: BAM to FASTQ | |
hisat2_align |
../tools/hisat2_align.cwl
(CommandLineTool)
|
HISAT2: align |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
fastqs | File[] | ||
aligned_bam | File |
Permalink:
https://w3id.org/cwl/view/git/f9600f9959acdc30259ba7e64de61104c9b01f0b/definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl