Workflow: mirna_profiling.cwl
Fetched 2023-01-12 07:15:33 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bam | File | ||
| mirbase_db | String | ||
| species_code | String | ||
| ucsc_database | String | ||
| awk_expression | String | ||
| project_directory | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| mirna_tcga |
../../tools/mirna_tcga.cwl
(CommandLineTool)
|
||
| mirna_annotate |
../../tools/mirna_annotate.cwl
(CommandLineTool)
|
||
| mirna_graph_libs |
../../tools/mirna_graph_libs.cwl
(CommandLineTool)
|
||
| samtools_bamtosam |
../../tools/samtools_view.cwl
(CommandLineTool)
|
||
| mirna_adapter_report |
../../tools/awk.cwl
(CommandLineTool)
|
||
| mirna_alignment_stats |
../../tools/mirna_alignment_stats.cwl
(CommandLineTool)
|
||
| mirna_expression_matrix |
../../tools/mirna_expression_matrix.cwl
(CommandLineTool)
|
||
| mirna_adapter_report_sorted |
../../tools/sort.cwl
(CommandLineTool)
|
||
| mirna_expression_matrix_mimat |
../../tools/mirna_expression_matrix_mimat.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| mirna_graph_libs_jpgs | Directory | ||
| mirna_tcga_mirnas_quant | File | ||
| mirna_tcga_isoforms_quant | File | ||
| mirna_alignment_stats_features | Directory | ||
| mirna_adapter_report_sorted_output | File | ||
| mirna_expression_matrix_expn_matrix_txt | File | ||
| mirna_expression_matrix_expn_matrix_norm_txt | File | ||
| mirna_expression_matrix_expn_matrix_norm_log_txt | File | ||
| mirna_expression_matrix_mimat_expn_matrix_mimat_txt | File | ||
| mirna_expression_matrix_mimat_expn_matrix_mimat_norm_txt | File | ||
| mirna_expression_matrix_mimat_expn_matrix_mimat_norm_log_txt | File |
Permalink:
https://w3id.org/cwl/view/git/0c1a40ea1efb1656644ccec0b7abe659539340e7/workflows/mirnaseq/mirna_profiling.cwl
