https://github.com/veupathdb/blat-nextflow
Nextflow Conversion of GenomeAlignWithGfClientTask
https://github.com/veupathdb/blat-nextflow
Last synced: 5 months ago
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Nextflow Conversion of GenomeAlignWithGfClientTask
- Host: GitHub
- URL: https://github.com/veupathdb/blat-nextflow
- Owner: VEuPathDB
- License: apache-2.0
- Created: 2022-07-22T19:57:35.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2025-04-01T20:19:03.000Z (about 1 year ago)
- Last Synced: 2025-08-06T09:50:38.765Z (11 months ago)
- Language: Nextflow
- Size: 39.1 KB
- Stars: 0
- Watchers: 16
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
THIS REPO IS 🚧 UNDER CONSTRUCTION 🚧 and NOT Used in ANY production CODE
# Nextflow Conversion of GenomeAlignWithGfClientTask
***
blat
***
```mermaid
flowchart TD
p0((Channel.fromPath))
p1([splitFasta])
p2(( ))
p3[blat:runBlat]
p4([collectFile])
p5(( ))
p0 --> p1
p1 -->|seqs| p3
p2 -->|data.2bit| p3
p3 --> p4
p4 --> p5
```
### Get Started
* Install Nextflow
`curl https://get.nextflow.io | bash`
## Usage
Main parameters:
| param | value type | description |
| ------------- | ------------- | ------------ |
| seqFile | string | Path to input fasta file |
| fastaSubsetSize | integer | How many sequences per split of input file |
| databasePath | string | Path to database Files |
| outputDir | string | publish directory |
| maxIntron | integer | Maximum intron size (Default 750000) |
| dbType | string | "dna" / "prot" / "dnax" (DNA sequence translated in six frames to protein). Default is dna. |
| queryType | string | "dna" / "prot" / "dnax" (DNA sequence translated in six frames to protein) "rnax" (DNA sequence translated in three frames to protein) |
| blatParams | string | Additional parameters for gfClient |
| trans | boolean | Translate database to protein in 6 frames |
### Example
`nextflow run https://github.com/VEuPathDB/blat -with-trace -c -r main`