66 lines
1.2 KiB
Plaintext
66 lines
1.2 KiB
Plaintext
#!/usr/bin/env nextflow
|
|
/*
|
|
* Copyright 2013-2024, Seqera Labs
|
|
*
|
|
* 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.
|
|
*/
|
|
|
|
params.in = "$baseDir/data/sample.fa"
|
|
SPLIT = (System.properties['os.name'] == 'Mac OS X' ? 'gcsplit' : 'csplit')
|
|
|
|
process split {
|
|
input:
|
|
path 'query.fa'
|
|
|
|
output:
|
|
path 'seq_*'
|
|
|
|
"""
|
|
$SPLIT query.fa '%^>%' '/^>/' '{*}' -f seq_
|
|
"""
|
|
}
|
|
|
|
|
|
process printTwo {
|
|
debug true
|
|
|
|
input:
|
|
path 'chunk'
|
|
|
|
output:
|
|
file 'chunk1:chunk3'
|
|
|
|
"""
|
|
cat chunk* | rev
|
|
"""
|
|
|
|
}
|
|
|
|
process printLast {
|
|
debug true
|
|
|
|
input:
|
|
file 'chunk'
|
|
|
|
output:
|
|
file 'chunk'
|
|
|
|
"""
|
|
cat chunk
|
|
"""
|
|
}
|
|
|
|
workflow {
|
|
split(params.in) | printTwo | flatten | printLast
|
|
}
|