Workflow: STAR-Alignment-PE
This workflow aligns the fastq files using STAR for paired-end samples
- 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/4b75136d8aca10fec5bf008191ceaae92b7c46fb/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 |
---|---|---|---|
stats_bam | File | ||
sorted_bam | File | ||
star_stats | File (Optional) | ||
mappingstats | File (Optional) | ||
readspergene | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/4b75136d8aca10fec5bf008191ceaae92b7c46fb/workflows/Alignments/star-alignment.cwl