Workflow: Compute library complexity
Fetched 2023-01-15 00:47:20 GMT
Verified with cwltool version 3.1.20221201130942
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:
Open Public License v1.0
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/265440c63ab75d2451c90bcd116e725626e9a608/workflows/File-formats/bedtools-bam-pbc.cwl
