Workflow: Short read alignment pipeline
Fetched 2025-04-27 08:15:22 GMT
Verified with cwltool version 3.1.20221201130942
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- Default Values
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- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| nthreads | Integer | Number of threads for alignment | |
| fastq_dir | Directory | Directory containing two FASTQ files | |
| hisat2_idx_basedir | Directory | HISAT2 index directory | |
| hisat2_idx_basename | String | HISAT2 index basename |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sort_bam |
alignment-steps/sort-bam.cwl
(CommandLineTool)
|
Sort BAM file | |
| align_reads |
alignment-steps/align-reads.cwl
(CommandLineTool)
|
Align reads with HISAT2 | |
| convert_to_bam |
alignment-steps/convert-to-bam.cwl
(CommandLineTool)
|
Convert SAM to BAM |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_bam | File | Sorted BAM file |
Permalink:
https://w3id.org/cwl/view/git/199c8db58114c2b0b37b62bde954f9a918d1f3a1/alignment-pipeline.cwl
