mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 00:02:04 +00:00
49 lines
2 KiB
Text
49 lines
2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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//include { GUNZIP } from '../../../modules/gunzip/main.nf'
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include { UNTAR as UNTAR1 } from '../../../../modules/untar/main.nf'
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include { UNTAR as UNTAR2 } from '../../../../modules/untar/main.nf'
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include { UNTAR as UNTAR3 } from '../../../../modules/untar/main.nf'
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include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/antismash/antismashlitedownloaddatabases/main.nf'
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include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/antismash/antismashlite/main.nf'
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include { PROKKA } from '../../../modules/prokka/main.nf'
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workflow test_antismashlite {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true) ]
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input_antismash_db1 = [
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[],
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file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
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]
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input_antismash_db2 = [
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[],
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file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
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]
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input_antismash_db3 = [
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[],
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file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
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]
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UNTAR1 ( input_antismash_db1 )
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UNTAR2 ( input_antismash_db2 )
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UNTAR3 ( input_antismash_db3 )
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ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] }, UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
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ANTISMASH_ANTISMASHLITE ( input, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database )
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}
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//workflow test_prokka_antismashlite {
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// input_gunzip = [ [ id:'test' ], // meta map
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// file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true) ]
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// GUNZIP ( input_gunzip )
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// PROKKA ( GUNZIP.out.gunzip, [], [] )
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// ANTISMASHLITEDOWNLOADDATABASES ()
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// ANTISMASH ( PROKKA.out.gbk )
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// }
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