- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
reads |
Reads to align |
||
idxbase | File |
Base filename of bwa index to map against |
|
blacklist | File |
Blacklist regions to remove |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
sort |
tools/samtools-sort.cwl
(CommandLineTool)
|
||
align |
tools/bwa-mem.cwl
(CommandLineTool)
|
||
to_bam |
tools/samtools-samtobam.cwl
(CommandLineTool)
|
||
mark_duplicates |
tools/picard-MarkDuplicates.cwl
(CommandLineTool)
|
||
remove_unmapped |
tools/samtools-view.cwl
(CommandLineTool)
|
||
remove_blacklist |
tools/bedtools-intersect.cwl
(CommandLineTool)
|
Outputs
ID | Type | Label | Doc |
---|---|---|---|
processed_reads | File |
Permalink:
https://w3id.org/cwl/view/git/f6346c109000c92ae53183df844eece0ad63eeb7/chipseq_tf_align.cwl