Workflow: Subsample BAM file creating a tagAlign and pseudoreplicates
Fetched 2023-01-09 00:09:28 GMT
Verified with cwltool version 3.1.20221201130942
This workflow creates a subsample from a BAM file creating a tagAlign and pseudoreplicates
- 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/b8f18a03ffbd7d5b78a7f220686b81d539686e98/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| nreads | Integer | ||
| bam_file | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gzip |
../../tools/basic/gzip.cwl
(CommandLineTool)
|
gzip |
Compress files |
| shuf |
../../tools/basic/shuf.cwl
(CommandLineTool)
|
shuf |
SHUF command |
| gzip_cat |
../../tools/basic/gzip.cwl
(CommandLineTool)
|
gzip |
Compress files |
| filter_chrM |
../../tools/basic/grep.cwl
(CommandLineTool)
|
grep |
GREP command |
| create_tagalign |
create-tagAlign.cwl
(Workflow)
|
Create tagAlign file |
This workflow creates tagAlign file |
| pseudoreplicate_gzip |
../../tools/basic/gzip.cwl
(CommandLineTool)
|
gzip |
Compress files |
| pseudoreplicate_split_file |
../../tools/basic/split_half.cwl
(CommandLineTool)
|
split |
SPLIT command |
| pseudoreplicate_count_lines |
../../tools/basic/wc.cwl
(CommandLineTool)
|
wc |
WC command |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| tagalign_out | File | ||
| subsample_out | File | ||
| pseudoreplicate_gzip_out | File[] |
Permalink:
https://w3id.org/cwl/view/git/b8f18a03ffbd7d5b78a7f220686b81d539686e98/workflows/File-formats/subample-pseudoreplicates.cwl
