ERROR ~ Ambiguous method overloading for method java.io.File#<init>.
Michał T. Lorenc
> nextflow run trinotate.nf --genome /home/lorencm/trinotate/Trinotate-3.0.2/sample_data/data/Trinity.fasta --chunks 4 --databases /home/lorencm/trinotate/databases/ --output /home/lorencm/trinotate/
N E X T F L O W ~ version 0.24.2
Launching `trinotate.nf` [modest_almeida] - revision: f67362ec61
T R I N O T A T E - N F ~ version 0.1
=====================================
genome : /home/lorencm/trinotate/Trinotate-3.0.2/sample_data/data/Trinity.fasta
databases : /home/lorencm/trinotate/databases/
chunks : 4
output : /home/lorencm/trinotate/
WARN: Access to undefined parameter `database` -- Initialise it to a default value eg. `params.database = some_value`
ERROR ~ Ambiguous method overloading for method java.io.File#<init>.
Cannot resolve which method to invoke for [null, class java.lang.String] due to overlapping prototypes between:
[class java.lang.String, class java.lang.String]
[class java.io.File, class java.lang.String]
#!/usr/bin/env nextflow
log.info "T R I N O T A T E - N F ~ version 0.1"
log.info "====================================="
log.info "genome : ${params.genome}"
log.info "databases : ${params.databases}"
log.info "chunks : ${params.chunks}"
log.info "output : ${params.output}"
log.info " \n"
/*
* Input parameters validation
*/
genome = file(params.genome)
swissProt = new File(params.databases, "uniprot_sprot.pep")
pfamA = new File(params.databases, "Pfam-A.hmm")
trinotateSqlite = new File(params.databases, "Trinotate_v3.sqlite")
chunks = params.chunks
//db_name = file(params.db).name
params.chunk = 1
Channel.fromPath(genome)
.splitFasta(by: params.chunk)
.set{chunks}
Channel.path(new File(params.database, "uniprot_sprot.pep"))
.set(swissProt)
process formatBlastDatabases {
input:
file prot from swissProt
output:
file "${dbName}.*" into blastDb
script:
dbName = species.baseName
"""
makeblastdb -dbtype prot -in ${swissProt} -out ${dbName}
"""
}
/*
* Extends a BLAST query for each entry in the 'chunks' channel
*/
process blast {
input:
file 'query.fa' from chunks
file db_path from blastdb
output:
file blast_results
"""
blastp -db $db_path -query query.fa -outfmt 6 > $params.database
"""
}