Workflow: sc_atac_seq_initial_analysis.cwl
Fetched 2026-02-17 08:58:18 GMT
Verified with cwltool version 3.1.20230201224320
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
GNU General Public License v3.0 only
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| assay | String | ||
| threads | Integer (Optional) | ||
| input_fastq1 | File | ||
| input_fastq2 | File | ||
| metadata_file | File (Optional) | ||
| orig_fastq_dir | Directory[] | ||
| concat_fastq_dir | Directory |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| adjust_barcodes |
adjust-barcodes.cwl
(CommandLineTool)
|
Assay-specific adjustment of cell barcodes | |
| convert_to_h5ad |
convert_to_h5ad.cwl
(CommandLineTool)
|
Assay-specific adjustment of cell barcodes | |
| create_fragment_file |
sc_atac_seq_process_steps/create_fragment_file.cwl
(CommandLineTool)
|
create fragment file |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam_file | File | ||
| bam_index | File | ||
| image_file | File | ||
| archr_project | Directory | ||
| fragment_file | File | ||
| TSS-vs-Frags_pdf | File | ||
| cell_by_bin_h5ad | File | ||
| cell_by_gene_h5ad | File | ||
| gene_row_data_csv | File | ||
| cell_column_data_csv | File | ||
| TSS_by_Unique_Frags_pdf | File | ||
| QC-Sample-Statistics_pdf | File | ||
| Fragment_Size_Distribution_pdf | File | ||
| QC-Sample-FragSizes-TSSProfile_pdf | File |
Permalink:
https://w3id.org/cwl/view/git/14985c972d540929cacbdf33925af2d4c6c9edb1/sc-atac-seq-pipeline/steps/sc_atac_seq_initial_analysis.cwl
