Workflow: sequence (bam or fastqs) to trimmed fastqs and HISAT alignments
- 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/889a077a20c0fdb01f4ed97aa4bc40f920c37a1a/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/889a077a20c0fdb01f4ed97aa4bc40f920c37a1a/definitions/subworkflows/sequence_to_trimmed_fastq_and_hisat_alignments.cwl