76 lines
1.4 KiB
Plaintext
76 lines
1.4 KiB
Plaintext
#!/usr/bin/env nextflow
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/*
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* Copyright 2013-2024, Seqera Labs
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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process align {
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publishDir 'data', mode: 'copy'
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input:
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val(x)
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output:
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path("*.bam")
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path("${x}.bai")
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"""
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echo ${x} > ${x}.bam
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echo ${x} | rev > ${x}.bai
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"""
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}
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process my_combine {
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publishDir 'data'
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publishDir 'more/data', mode: 'copy'
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input:
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path(bamfile)
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path(baifile)
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output:
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path 'result.txt'
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"""
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cat $bamfile > result.txt
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cat $baifile >> result.txt
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"""
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}
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process foo {
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publishDir 'data', mode: 'link'
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output:
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file 'xxx'
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'''
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mkdir xxx
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touch xxx/A
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touch xxx/B
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touch xxx/C
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'''
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}
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workflow {
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def input = Channel.of('alpha','beta','delta')
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align(input)
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def bam = align.out[0].toSortedList { it.name }
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def bai = align.out[1].toSortedList { it.name }
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my_combine( bam, bai )
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my_combine.out.view{ it.text }
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foo()
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}
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