Workflow: tinyrna_wf.cwl
Fetched 2026-02-06 18:39:10 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- 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 |
|---|---|---|---|
| best | Boolean (Optional) | ||
| ebwt | String | ||
| nofw | Boolean (Optional) | ||
| norc | Boolean (Optional) | ||
| ntoa | Boolean (Optional) | ||
| seed | Integer (Optional) | ||
| in_fq | File[] | ||
| k_aln | Integer (Optional) | ||
| noref | Boolean (Optional) | ||
| trim3 | Integer (Optional) | ||
| trim5 | Integer (Optional) | ||
| solexa | Boolean (Optional) | ||
| strata | Boolean (Optional) | ||
| 3p_trim | Integer (Optional) | ||
| 5p_trim | Integer (Optional) | ||
| all_aln | Boolean (Optional) | ||
| no_unal | Boolean (Optional) | ||
| offrate | Integer (Optional) | ||
| seedlen | Integer (Optional) | ||
| seedmms | Integer (Optional) | ||
| threads | Integer (Optional) | ||
| compress | Boolean (Optional) | ||
| run_name | String | ||
| solexa13 | Boolean (Optional) | ||
| ftabchars | Integer (Optional) | ||
| gff_files | File[] (Optional) | ||
| plot_pval | Float (Optional) | ||
| run_deseq | Boolean | ||
| threshold | Integer (Optional) | ||
| bt_phred64 | Boolean (Optional) | ||
| end_to_end | Integer (Optional) | ||
| fp_phred64 | Boolean (Optional) | ||
| paths_file | File | ||
| trim_tail1 | Integer (Optional) | ||
| compression | Integer (Optional) | ||
| in_pipeline | Boolean (Optional) | ||
| samples_csv | File | ||
| trim_front1 | Integer (Optional) | ||
| trim_poly_x | Boolean (Optional) | ||
| aligned_seqs | File[] (Optional) | ||
| dge_pca_plot | Boolean (Optional) | ||
| features_csv | File | ||
| length_limit | Integer (Optional) | ||
| n_base_limit | Integer (Optional) | ||
| suppress_aln | Integer (Optional) | ||
| adapter_fasta | File (Optional) | ||
| counter_diags | Boolean (Optional) | ||
| dge_drop_zero | Boolean (Optional) | ||
| plot_requests | String[] | ||
| shared_memory | Boolean (Optional) | ||
| bt_index_files | File[] | ||
| dir_name_fastp | String | ||
| dont_overwrite | Boolean (Optional) | ||
| poly_x_min_len | Integer (Optional) | ||
| dir_name_bowtie | String | ||
| dir_name_config | String | ||
| length_required | Integer (Optional) | ||
| adapter_sequence | String (Optional) | ||
| plot_style_sheet | File (Optional) | ||
| run_bowtie_build | Boolean | ||
| sample_basenames | String[] | ||
| control_condition | String (Optional) | ||
| dir_name_bt_build | String | ||
| plot_len_dist_max | Integer (Optional) | ||
| plot_len_dist_min | Integer (Optional) | ||
| counter_decollapse | Boolean (Optional) | ||
| counter_stepvector | String (Optional) | ||
| dir_name_tiny-plot | String | ||
| plot_unknown_class | String (Optional) | ||
| plot_vector_points | Boolean (Optional) | ||
| dir_name_tiny-count | String | ||
| dir_name_tiny-deseq | String | ||
| fastp_report_titles | String[] | ||
| plot_dge_scatter_max | Double (Optional) | ||
| plot_dge_scatter_min | Double (Optional) | ||
| processed_run_config | File | ||
| plot_unassigned_class | String (Optional) | ||
| dir_name_tiny-collapse | String | ||
| reference_genome_files | File[] | ||
| qualified_quality_phred | Integer (Optional) | ||
| counter_mismatch_pattern | String (Optional) | ||
| disable_adapter_trimming | Boolean (Optional) | ||
| disable_length_filtering | Boolean (Optional) | ||
| disable_quality_filtering | Boolean (Optional) | ||
| unqualified_percent_limit | Integer (Optional) | ||
| overrepresentation_analysis | Boolean (Optional) | ||
| overrepresentation_sampling | Integer (Optional) | ||
| counter_normalize_by_feature_hits | Boolean (Optional) | ||
| counter_normalize_by_genomic_hits | Boolean (Optional) | ||
| plot_class_scatter_filter_exclude | String[] (Optional) | ||
| plot_class_scatter_filter_include | String[] (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bowtie |
../tools/bowtie.cwl
(CommandLineTool)
|
||
| tiny-plot |
../tools/tiny-plot.cwl
(CommandLineTool)
|
||
| tiny-count |
../tools/tiny-count.cwl
(CommandLineTool)
|
||
| tiny-deseq |
../tools/tiny-deseq.cwl
(CommandLineTool)
|
||
| preprocessing |
preprocessing.cwl
(Workflow)
|
||
| organize_fastp |
../tools/make-subdir.cwl
(ExpressionTool)
|
||
| organize_bowtie |
../tools/make-subdir.cwl
(ExpressionTool)
|
||
| organize_config |
../tools/make-subdir.cwl
(ExpressionTool)
|
||
| bt_build_optional |
../tools/bowtie-build.cwl
(CommandLineTool)
|
||
| organize_tiny-plot |
../tools/make-subdir.cwl
(ExpressionTool)
|
||
| organize_bt_indexes |
../tools/make-subdir.cwl
(ExpressionTool)
|
||
| organize_tiny-count |
../tools/make-subdir.cwl
(ExpressionTool)
|
||
| organize_tiny-deseq |
../tools/make-subdir.cwl
(ExpressionTool)
|
||
| organize_tiny-collapse |
../tools/make-subdir.cwl
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| fastp_out_dir | Directory | ||
| bowtie_out_dir | Directory | ||
| config_out_dir | Directory | ||
| bt_build_out_dir | Directory (Optional) | ||
| tiny-plot_out_dir | Directory | ||
| tiny-count_out_dir | Directory | ||
| tiny-deseq_out_dir | Directory (Optional) | ||
| tiny-collapse_out_dir | Directory |
Permalink:
https://w3id.org/cwl/view/git/943cb16fc421f0a37df3619086cbd0330c78174e/tiny/cwl/workflows/tinyrna_wf.cwl
