- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
BSD 2-clause "Simplified" License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
sample | String (Optional) | ||
library | String (Optional) | ||
threads | Integer (Optional) | ||
platform | String (Optional) | ||
readgroup | String (Optional) | ||
reference | File | ||
chunk_size | Integer (Optional) | ||
input_reads | File[] | ||
output_file | String | ||
sort_threads | Integer (Optional) | ||
extract_chunks | String[] | ||
mark_secondary | Boolean (Optional) | ||
sort_reference | File (Optional) | ||
bam_compression | Integer (Optional) | ||
min_std_max_min | Integer[] (Optional) | ||
advanced_options | String[] (Optional) | ||
minimum_seed_length | Integer (Optional) | ||
input_reads_index_file | File |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
bwa |
../algo/bwa-mem-sort-with-fastq-slicer.cwl
(CommandLineTool)
|
||
merge |
../algo/bam-merge.cwl
(CommandLineTool)
|
merge sorted bam files. If input bam files are in the order of coordinate, and no overlap, mergemode 10 can be used |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
output | File |
Permalink:
https://w3id.org/cwl/view/git/d20382adfe7285cb517a25d95d2bcb7586546e23/stage/bwa-mem-sort-distr.cwl