Workflow: magicblast-alignment-pe
Fetched 2026-04-15 18:52:34 GMT
Verified with cwltool version 3.1.20230201224320
This workflow aligns the fastq files using magicblast 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/master/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| db | String | ||
| dbdir | Directory | ||
| query | File | ||
| threads | Integer | ||
| query_mate | 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/magicblast/magicblast.cwl
(CommandLineTool)
|
Magicblast |
NCBI Magicblast |
| 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 |
| samtools_view |
../../tools/samtools/samtools-view.cwl
(CommandLineTool)
|
Samtools-view |
Samtools is a suite of programs for interacting with high-throughput sequencing data |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| stats_bam | File | ||
| sorted_bam | File | ||
| out_unaligned_output | File |
Permalink:
https://w3id.org/cwl/view/git/b5a440939ac6022ee81aeeb0dd7daf3983228a61/workflows/Alignments/magicblast-alignment.cwl
