https://github.com/veupathdb/bowtie-mapping-nextflow
Nextflow conversion of BowtieMappingTask
https://github.com/veupathdb/bowtie-mapping-nextflow
Last synced: 4 months ago
JSON representation
Nextflow conversion of BowtieMappingTask
- Host: GitHub
- URL: https://github.com/veupathdb/bowtie-mapping-nextflow
- Owner: VEuPathDB
- License: mit
- Created: 2022-06-06T14:04:59.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2025-06-26T16:34:38.000Z (12 months ago)
- Last Synced: 2025-09-10T10:17:06.912Z (10 months ago)
- Language: Nextflow
- Size: 36.1 MB
- Stars: 0
- Watchers: 16
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
THIS REPO IS 🚧 UNDER CONSTRUCTION 🚧 and NOT Used in ANY production CODE
# bowtieMapping
***
bowtieMapping (From sra download)
***
```mermaid
flowchart TD
p0((Channel.fromList))
p1[bowtieMapping:sra:downloadFiles]
p2(( ))
p3(( ))
p4[bowtieMapping:sra:bowtie]
p5[bowtieMapping:sra:PCRDuplicates]
p6(( ))
p0 -->|ids| p1
p1 --> p4
p2 -->|indexfiles| p4
p3 -->|indexFileBasename| p4
p4 --> p5
p5 --> p6
```
***
bowtieMapping (from local files)
***
```mermaid
flowchart TD
p0((Channel.fromFilePairs))
p1(( ))
p2(( ))
p3[bowtieMapping:local:bowtie]
p4[bowtieMapping:local:PCRDuplicates]
p5(( ))
p0 -->|files| p3
p1 -->|indexfiles| p3
p2 -->|indexFileBasename| p3
p3 --> p4
p4 --> p5
```
Description of nextflow configuration parameters:
| param | value type | description |
| ------------- | ------------- | ------------ |
| inputFilePath | string | Path to input file |
| outputDir | string | Path to where you would like output files stored |
| databaseFasta | string | Path to the fasta file that you would like to use a the database for Psipred |
| preconfiguredDatabase | boolean | Are you using a preconfigured database? |
| writeBedFile | boolean | If you would like to output an additional bedfile. |
| isSingleEnd | boolean | Is the data single-end or paired-end? |
| isColorspace | boolean | Is the data colorspace data? |
| removePCRDuplicates | boolean | Would you like PCR duplicates removed? |
| input | path | Path to input tsv file if downloading from sra or path to directory holding input files |
| downloadMethod | string | Either 'sra' or 'local' |
| databaseFileDir | path | Path to database file dir|
| indexFileBasename | string | Basename for bt2 files. Ex "index" if files start index.1.bt2, index.2.bt2, etc |
| mateAQual | path | Path to qual file for mateA |
| mateBQual | path | Path to qual fiel for mateB |
### Get Started
* Install Nextflow
`curl https://get.nextflow.io | bash`
* Run the script
`nextflow run VEuPathDB/blastSimilarity -with-trace -c -r main`