Workflow: Short read alignment pipeline
Fetched 2023-01-12 19:32:35 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 | Launch `nthreads` parallel search threads |
Launch `nthreads` parallel search threads (default: 1). Threads will run on separate processors/cores and synchronize when parsing reads and outputting alignments. Searching for alignments is highly parallel, and speedup is close to linear. Increasing -p increases HISAT2's memory footprint. |
| fastq_dir | Directory | Directory containing two FASTQ files | |
| hisat2_idx_basedir | Directory | Path to directory containing the reference index |
Path to directory containing the reference index |
| hisat2_idx_basename | String | Basename of the hisat2 index files |
Basename of the hisat2 index files, not including extensions like .1.ht2 |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sort_bam |
alignment-steps/sort-bam.cwl
(CommandLineTool)
|
Sort BAM file | |
| align_reads |
alignment-steps/align-reads.cwl
(CommandLineTool)
|
||
| 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/a1bd61e9b4000cbc12e36f686e9ffe0e5e8fe348/alignment-pipeline.cwl
