THIS REPO IS 🚧 UNDER CONSTRUCTION 🚧 and NOT Used in ANY production CODE
blat
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
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Install Nextflow
curl https://get.nextflow.io | bash
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 |
nextflow run https://github.com/VEuPathDB/blat -with-trace -c <config_file> -r main
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