blast.nf

#!/usr/bin/env nextflow
/*
 * Copyright 2020-2022, Seqera Labs
 * Copyright 2013-2019, Centre for Genomic Regulation (CRG)
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
nextflow.enable.dsl=1

params.db = "$baseDir/blast-db/tiny"
params.query = "$baseDir/data/sample.fa"
params.chunkSize = 1

DB = file(params.db)

seq = Channel .fromPath(params.query) .splitFasta( by: params.chunkSize )

process blast {
    input:
    file 'seq.fa' from seq

    output:
    file 'out' into blast_result

    """
    blastp -db $DB -query seq.fa -outfmt 6 > out
    """
}

process sort {
    input:
    file 'hits_*' from blast_result.collect()

    output:
    stdout result

    """
    sort hits_*
    """
}


result.subscribe { println it }