Workflow: create_snap_and_analyze.cwl
Fetched 2025-08-26 03:44:14 GMT
Verified with cwltool version 3.1.20230201224320
- 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 |
|---|---|---|---|
| threads | Integer (Optional) | ||
| promoters | File (Optional) | ||
| gene_track | File (Optional) | ||
| size_index | File (Optional) | ||
| tmp_folder | String (Optional) | ||
| genome_name | String (Optional) | ||
| bin_size_list | Integer[] (Optional) | ||
| alignment_index | File (Optional) | ||
| gene_annotation | File (Optional) | ||
| encode_blacklist | File (Optional) | ||
| preferred_barcodes | File (Optional) | ||
| sequence_directory | Directory | ||
| reference_genome_fasta | File (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fastqc |
fastqc.cwl
(CommandLineTool)
|
Runs fastQC on each fastq file in fastq directory | |
| create_and_analyze_snap_file |
steps/snaptools_create_snap_file.cwl
(Workflow)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam_file | File[] | ||
| snap_file | File[] | ||
| fastqc_dir | Directory | ||
| snap_qc_file | File[] | ||
| fragment_file | File[] | ||
| motif_CSV_files | d86eaff4845cc447ca9425c5d8de5fa5[] | ||
| motif_RData_file | File[] | ||
| analysis_BED_files | 95b400e36e8f31f56a82c5765214c28c[] | ||
| analysis_CSV_files | 0dfd48cea896a7c1fb70b3811791968c[] | ||
| analysis_MTX_files | a97e6e73c4859e5935e513d90c7fb6b0[] | ||
| analysis_PDF_files | d52a144a2d8ca3e8e00879e1a65160a4[] | ||
| analysis_TXT_files | 113a94e54e84309a74bfb0fcdaba40af[] | ||
| alignment_qc_report | File[] | ||
| analysis_HDF5_files | 8643b22e06024bfed54d78a32ddbb492[] | ||
| analysis_RDS_objects | 8d4691caaacb88633979b71ec5999811[] |
Permalink:
https://w3id.org/cwl/view/git/302f1f3c019b74b85a4decc56c0793726e99c191/create_snap_and_analyze.cwl
