- 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 | ||
max_uncalled | Integer | ||
read_group_id | String | ||
min_readlength | Integer | ||
reference_index | String | ||
adapter_trim_end | String | ||
adapter_min_overlap | Integer |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
index_bam |
../tools/index_bam.cwl
(CommandLineTool)
|
samtools index | |
trim_fastq |
../tools/trim_fastq.cwl
(CommandLineTool)
|
Trim FASTQ (flexbar) | |
bam_to_fastq |
../tools/bam_to_fastq.cwl
(CommandLineTool)
|
Picard: BAM to FASTQ | |
biscuit_align |
../tools/biscuit_align.cwl
(CommandLineTool)
|
Biscuit: align | |
biscuit_markdup |
../tools/biscuit_markdup.cwl
(CommandLineTool)
|
Biscuit dedup |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
aligned_bam | File |
Permalink:
https://w3id.org/cwl/view/git/d3e4bf55753cd92f97537c7d701187ea92d1e5f0/definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl