Workflow: sc_atac_seq_process_and_analyze.cwl
Fetched 2024-05-20 11:35:54 GMT
Verified with cwltool version 3.1.20230201224320
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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) | ||
| input_fastq1 | File | ||
| input_fastq2 | File | ||
| 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 | ||
| peaks_bed | File | ||
| fragment_file | File | ||
| TSS-vs-Frags_pdf | File | ||
| cell_by_bin_h5ad | File | ||
| gene_markers_csv | File (Optional) | ||
| peak_markers_csv | File | ||
| cell_by_gene_h5ad | File | ||
| gene_row_data_csv | File | ||
| cell_column_data_csv | File | ||
| Peak-Call-Summary_pdf | File | ||
| Peak-Marker-Heatmap_pdf | File (Optional) | ||
| TSS_by_Unique_Frags_pdf | File | ||
| QC-Sample-Statistics_pdf | File | ||
| umap_coords_clusters_csv | File | ||
| GeneScores-Marker-Heatmap_pdf | File (Optional) | ||
| Plot-UMAP-Sample-Clusters_pdf | File | ||
| Fragment_Size_Distribution_pdf | File | ||
| QC-Sample-FragSizes-TSSProfile_pdf | File |
Permalink:
https://w3id.org/cwl/view/git/d0e845df600fff7944943e2520db7a0cda8d00db/steps/sc_atac_seq_process_and_analyze.cwl
