Workflow: chromVAR scATAC-seq pipeline
Fetched 2025-04-26 22:18:14 GMT
Verified with cwltool version 3.1.20221201130942
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Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| nthreads | Integer | Number of threads for alignment | |
| fastq_directories | Directory[] | FASTQ parent directory | |
| hisat2_idx_basedir | Directory | HISAT2 index directory | |
| hisat2_idx_basename | String | HISAT2 index basename | |
| output_plot_filename | String | Motif enrichment output filename (.pdf) | |
| output_rdata_filename | String | chromVAR workspace output filename (.RData) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| chromvar |
steps/chromvar.cwl
(CommandLineTool)
|
Run chromVAR | |
| call_peaks |
steps/call-peaks.cwl
(CommandLineTool)
|
Call peaks with Genrich | |
| 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/199c8db58114c2b0b37b62bde954f9a918d1f3a1/chromvar-pipeline.cwl
