Workflow: ATAC-seq pipeline
Fetched 2026-07-14 12:36:28 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| nthreads | Integer | Launch `nthreads` parallel search threads |
Launch `nthreads` parallel search threads (default: 1). Threads will run on separate processors/cores and synchronize when parsing reads and outputting alignments. Searching for alignments is highly parallel, and speedup is close to linear. Increasing -p increases HISAT2's memory footprint. |
| fastq_directories | Directory[] | Directory containing subdirs for paired FASTQ files | |
| hisat2_idx_basedir | Directory | Path to directory containing the reference index |
Path to directory containing the reference index |
| hisat2_idx_basename | String | Basename of the hisat2 index files |
Basename of the hisat2 index files, not including extensions like .1.ht2 |
| output_plot_filename | String | ||
| output_rdata_filename | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| chromvar |
steps/chromvar.cwl
(CommandLineTool)
|
||
| call_peaks |
steps/call-peaks.cwl
(CommandLineTool)
|
||
| merge_bams |
steps/merge-bams.cwl
(CommandLineTool)
|
Merge BAM files | |
| align_reads |
alignment-pipeline.cwl
(Workflow)
|
Short read alignment pipeline |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| plot_output | File | ||
| rdata_output | File |
Permalink:
https://w3id.org/cwl/view/git/a1bd61e9b4000cbc12e36f686e9ffe0e5e8fe348/chromvar-pipeline.cwl
