- 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/5465f666aac446a6d66fed1819e48a79395f6b02/steps/snaptools_create_snap_file.cwl