Workflow: chromVAR scATAC-seq pipeline
Fetched 2023-01-12 13:00:40 GMT
Verified with cwltool version 3.1.20221201130942
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- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| nthreads | Integer | Number of threads for alignment | |
| fastq_directories | Directory[] | Directory containing subdirs for paired FASTQ files | |
| hisat2_idx_basedir | Directory | HISAT2 index directory | |
| hisat2_idx_basename | String | HISAT2 index basename | |
| output_plot_filename | String | Plot of differential motif enrichment | |
| output_rdata_filename | String | RData file containing chromVAR analysis workspace |
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/eb4c7911d3a6d9fc929eda11e1e03d74b0469cb9/chromvar-pipeline.cwl
