Workflow: create_snap_and_analyze.cwl
Fetched 2024-11-26 06:12:23 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
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- 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) | ||
| promoters | File (Optional) | ||
| gene_track | File (Optional) | ||
| size_index | File (Optional) | ||
| tmp_folder | String (Optional) | ||
| exclude_bam | Boolean (Optional) | ||
| genome_name | String (Optional) | ||
| bin_size_list | Integer[] (Optional) | ||
| blacklist_bed | File (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 |
steps/fastqc.cwl
(CommandLineTool)
|
Runs fastQC on each fastq file in fastq directory | |
| maybe_save_bam_file |
3d795d40cbbecfb33d8ea896949cf461
(ExpressionTool)
|
||
| create_and_analyze_snap_file |
steps/snaptools_create_snap_file.cwl
(Workflow)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam_file | File (Optional) | ||
| snap_file | File | ||
| fastqc_dir | Directory[] | ||
| snap_qc_file | File | ||
| fragment_file | File | ||
| cell_by_bin_mtx | File | ||
| motif_CSV_files | File[] | ||
| cell_by_bin_bins | File | ||
| cell_by_bin_h5ad | File | ||
| motif_RData_file | File | ||
| cell_by_gene_h5ad | File | ||
| analysis_BED_files | File[] | ||
| analysis_CSV_files | File[] | ||
| analysis_PDF_files | File[] | ||
| alignment_qc_report | File | ||
| cell_by_gene_matrix | File | ||
| analysis_RDS_objects | File[] | ||
| cell_by_bin_barcodes | File |
Permalink:
https://w3id.org/cwl/view/git/44dbe381f68878ab607b167b62267c4ea97f3322/create_snap_and_analyze.cwl
