Workflow: create_snap_and_analyze.cwl
Fetched 2024-11-24 05:54:57 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 | bb70e0d5e7f09a890bf9d6e4ee5f5f82[] | ||
| motif_RData_file | File[] | ||
| analysis_BED_files | bc0379ab71f3553d539947a32ca7c3a5[] | ||
| analysis_CSV_files | 55dcd9c38198ec3a5f3e66bde28285f9[] | ||
| analysis_MTX_files | b07bde6ebc28d17ed31febc621bc8483[] | ||
| analysis_PDF_files | 9ec04c88382ec3aaf069246562bacf17[] | ||
| analysis_TXT_files | 472f8b2659fd9a3ed62154c6bea406dc[] | ||
| alignment_qc_report | File[] | ||
| analysis_HDF5_files | a4481f0841ca28f32a91800cf7aa2a1e[] | ||
| analysis_RDS_objects | 398f520c6922d03babcc39406e6c7ba5[] |
Permalink:
https://w3id.org/cwl/view/git/102d8cb180bb201d6ef054531a84a764a06c8622/create_snap_and_analyze.cwl
