Workflow: sc_atac_seq_prep_process_analyze.cwl
Fetched 2024-05-09 06:51:54 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:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| assay | String | ||
| threads | Integer (Optional) | ||
| exclude_bam | Boolean (Optional) | ||
| sequence_directory | Directory[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fastqc |
steps/fastqc.cwl
(CommandLineTool)
|
Runs fastQC on each fastq file in fastq directory | |
| maybe_save_bam_file |
be1ce94b3c5710f9886ed99ff2d16112
(ExpressionTool)
|
||
| sc_atac_seq_process_and_analyze |
steps/sc_atac_seq_process_and_analyze.cwl
(Workflow)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam_file | File (Optional) | ||
| fastqc_dir | Directory[] | ||
| 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 | ||
| genome_build_json | 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/sc_atac_seq_prep_process_analyze.cwl
