Workflow: Compute library complexity
This workflow compute library complexity
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/ncbi/cwl-ngs-workflows-cbb/527251ebb77750d02dcc9a370d978a153fc9328f/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
bam_file | File |
BAM file to be analyzed |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
sort |
../../tools/basic/sort.cwl
(CommandLineTool)
|
sort |
SORT command |
uniq |
../../tools/basic/uniq.cwl
(CommandLineTool)
|
uniq |
UNIQ command |
bamtobed |
../../tools/bedtools/bedtools-bamtobed.cwl
(CommandLineTool)
|
bedtools-bamtobed |
The bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks |
count_awk |
../../tools/basic/awk.cwl
(CommandLineTool)
|
awk |
AWK command |
first_awk |
../../tools/basic/awk.cwl
(CommandLineTool)
|
awk |
AWK command |
filter_chrM |
../../tools/basic/grep.cwl
(CommandLineTool)
|
grep |
GREP command |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
out | File |
Permalink:
https://w3id.org/cwl/view/git/527251ebb77750d02dcc9a370d978a153fc9328f/workflows/File-formats/bedtools-bam-pbc.cwl