Workflow: Transcriptome Read assignment
Fetched 2023-01-10 11:54:23 GMT
Verified with cwltool version 3.1.20221201130942
This workflow download SRA samples and aligng them to a transcriptome fasta file
- 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/de6380d83f9209e95559e66cf64ded3bf0e410ea/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| reads_1 | File | ||
| reads_2 | File | ||
| threads | Integer | ||
| genome_fasta | File |
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 |
| star_genome_indexes |
transcriptome-read-assignment.cwl#star_genome_indexes/a46af6c3-299f-4bbe-a447-100362817092
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| stats_bam | File | ||
| sorted_bam | File | ||
| star_stats | File (Optional) | ||
| indexed_bam | File | ||
| readspergene | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/de6380d83f9209e95559e66cf64ded3bf0e410ea/workflows/Annotation/transcriptome-read-assignment.cwl
