Workflow: STAR-Alignment-PE-circRNA
Fetched 2023-10-22 20:01:54 GMT
Verified with cwltool version 3.1.20230201224320
This workflow aligns the fastq files using STAR for paired-end samples to be used in circRNA pipeline
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/ncbi/cwl-ngs-workflows-cbb/1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| reads | File[] | ||
| threads | Integer | ||
| genomeDir | Directory | ||
| ramMaxSTAR | Float (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bam_sort |
../../tools/samtools/samtools-sort.cwl
(CommandLineTool)
|
Samtools-sort |
Samtools is a suite of programs for interacting with high-throughput sequencing data |
| alignment |
../../tools/star/star.cwl
(CommandLineTool)
|
STAR |
Spliced Transcripts Alignment to a Reference |
| bam_index |
../../tools/samtools/samtools-index.cwl
(CommandLineTool)
|
Samtools-index |
Samtools is a suite of programs for interacting with high-throughput sequencing data |
| bam_stats |
../../tools/samtools/samtools-stats.cwl
(CommandLineTool)
|
Samtools-stats |
Samtools is a suite of programs for interacting with high-throughput sequencing data |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| chimeric | File (Optional) | ||
| stats_bam | File | ||
| bamRemDups | File (Optional) | ||
| sorted_bam | File | ||
| star_stats | File (Optional) | ||
| mappingstats | File (Optional) | ||
| readspergene | File (Optional) | ||
| alignment_bam | File (Optional) | ||
| transcriptomesam | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49/workflows/Alignments/star-alignment-circRNA-default.cwl
