- 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 |
---|---|---|---|
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