- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
job_uuid | String | ||
input_bam | File | ||
reference | File | ||
interval_bed | File |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
bam_sort |
../../tools/harmonization/sambamba_sort.cwl
(CommandLineTool)
|
||
bam_reheader |
../../tools/harmonization/samtools_reheader.cwl
(CommandLineTool)
|
||
bam_to_fastq |
../../tools/harmonization/bam_to_fastq.cwl
(CommandLineTool)
|
||
trim_adaptor |
../../tools/harmonization/trimmomatic.cwl
(CommandLineTool)
|
||
readgroups_merge |
../../tools/harmonization/sambamba_merge.cwl
(CommandLineTool)
|
||
get_bam_new_header |
../../tools/harmonization/get_bam_new_header.cwl
(CommandLineTool)
|
||
get_readgroup_info |
../../tools/harmonization/get_readgroup_name.cwl
(CommandLineTool)
|
||
bwa_mem_filter_dedup |
../../tools/harmonization/bwa_mem.cwl
(CommandLineTool)
|
Outputs
ID | Type | Label | Doc |
---|---|---|---|
sorted_bam | File | ||
time_metrics_from_sort | File | ||
time_metrics_from_merge | File | ||
time_metrics_from_reheader | File | ||
time_metrics_from_bam_to_fastq | File | ||
time_metrics_from_trim_adaptor | File[] | ||
time_metrics_from_bwa_mem_filter_dedup | File[] |
Permalink:
https://w3id.org/cwl/view/git/1595f2bc453663c9e71c1a2d60729f481921029e/genomel/cwl/workflows/harmonization/harmonization_bwa_mem.cwl