Workflow: step4: STAR for CAGE-Seq reads analysis
Fetched 2026-05-14 22:10:17 GMT
Verified with cwltool version 3.1.20230201224320
STAR for CAGE-Seq reads analysis
- 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 |
|---|---|---|---|
| star_threads | Integer | threads for star |
threads for star |
| star_index_dir | Directory | STAR index directory |
STAR index directory |
| cage_seq_reads_1 | File[] [null] | CAGE-Seq reads 1 |
CAGE-Seq reads 1 |
| cage_seq_reads_2 | File[] [null] | CAGE-Seq reads 2 |
CAGE-Seq reads 2 |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| star_analysis_pe |
../Tools/05_star4cageseq_analysis_pe.cwl
(CommandLineTool)
|
run STAR for CAGE-Seq analysis (paired-end) |
Mapping the reads to the genome using STAR (STAR version 2.7.11b) for paired-end CAGE-seq data |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| sj_tab_files | File[] [null] | STAR splice junctions tab files |
STAR splice junctions tab files |
| main_log_files | File[] [null] | STAR main log files |
STAR main log files |
| final_log_files | File[] [null] | STAR final log files |
STAR final log files |
| log_stderr_files | File[] [null] | STAR stderr files |
STAR stderr files |
| log_stdout_files | File[] [null] | STAR stdout files |
STAR stdout files |
| aligned_bam_files | File[] [null] | STAR aligned BAM files |
STAR aligned BAM files |
| progress_log_files | File[] [null] | STAR progress log files |
STAR progress log files |
Permalink:
https://w3id.org/cwl/view/git/9728a86f7b73f7657a1f261e77a14ca59bdd561b/workflow/03_star4cageseq_analysis_subworkflow_pe.cwl
