Workflow: create_snap_and_analyze.cwl
Fetched 2024-11-25 11:32:41 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 | d554b7308412b25bb2817b5ac18e8927[] | ||
| motif_RData_file | File[] | ||
| analysis_BED_files | 99c780a54830d0c99dde50f87a037251[] | ||
| analysis_CSV_files | 2b2205225b14d4bd0411bbc7cb6299e2[] | ||
| analysis_MTX_files | ddd2a4ad5ca8940b863a2c1e20ab5588[] | ||
| analysis_PDF_files | 3772f78ae41d14f2e56613d5cafa324b[] | ||
| analysis_TXT_files | bb1cb62d6b814baef56db4976fa21fc1[] | ||
| alignment_qc_report | File[] | ||
| analysis_HDF5_files | a61d408cc25f3d50f78e5babcb111339[] | ||
| analysis_RDS_objects | 83168ff97cd59e5b7bfc1c6266f7aae9[] |
Permalink:
https://w3id.org/cwl/view/git/102d8cb180bb201d6ef054531a84a764a06c8622/create_snap_and_analyze.cwl
