Workflow: snaptools_create_snap_file.cwl
Fetched 2023-01-03 22:43:26 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| assay | String | ||
| threads | Integer (Optional) | ||
| processes | Integer (Optional) | ||
| promoters | File (Optional) | ||
| gene_track | File (Optional) | ||
| size_index | File (Optional) | ||
| tmp_folder | String (Optional) | ||
| genome_name | String (Optional) | ||
| input_fastq1 | File | ||
| input_fastq2 | File | ||
| bin_size_list | Integer[] (Optional) | ||
| blacklist_bed | File (Optional) | ||
| alignment_index | File (Optional) | ||
| gene_annotation | File (Optional) | ||
| concat_fastq_dir | Directory | ||
| encode_blacklist | File (Optional) | ||
| preferred_barcodes | File (Optional) | ||
| reference_genome_fasta | File (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| adjust_barcodes |
adjust-barcodes.cwl
(CommandLineTool)
|
Assay-specific adjustment of cell barcodes | |
| snapanalysis_setup_and_analyze |
snapanalysis_setup_and_analyze.cwl
(Workflow)
|
||
| snaptools_create_fragment_file |
create_snap_steps/snaptools_create_fragment_file.cwl
(CommandLineTool)
|
snaptools create fragment file |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam_file | File | ||
| snap_file | File | ||
| snap_qc_file | File | ||
| fragment_file | File | ||
| peaks_bed_file | File | ||
| motif_CSV_files | File[] | ||
| umap_coords_csv | File | ||
| cell_by_bin_h5ad | File | ||
| motif_RData_file | File | ||
| cell_by_gene_h5ad | File | ||
| analysis_CSV_files | File[] | ||
| analysis_PDF_files | File[] | ||
| analysis_RDS_objects | File[] |
Permalink:
https://w3id.org/cwl/view/git/e1af1eb62aa9f757bded9b995411d25e098b3572/steps/snaptools_create_snap_file.cwl
