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https://github.com/MillironX/nf-core_modules.git
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107 lines
4.1 KiB
Text
107 lines
4.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/antismash/antismashlite/main.nf'
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include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/antismash/antismashlitedownloaddatabases/main.nf'
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include { GUNZIP as GUNZIP1 } from '../../../../modules/gunzip/main.nf'
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include { GUNZIP as GUNZIP2 } 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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workflow test_antismashlite {
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genome_fna = [
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[ id:'test' ],
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file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
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]
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genome_gff = [
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[],
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file(params.test_data['bacteroides_fragilis']['genome']['genome_gff_gz'], checkIfExists: true)
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]
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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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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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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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// input_db = [
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// file('/home/jasmin/antismash_db/', checkIfExists: true)
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// ]
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// input_dir = [
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// file('/home/jasmin/antismash_dir/', checkIfExists: true)
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// ]
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GUNZIP1 ( genome_fna )
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GUNZIP2 ( genome_gff )
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UNTAR1 ( antismash_db1 )
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UNTAR2 ( antismash_db2 )
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UNTAR3 ( 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 ( GUNZIP1.out.gunzip, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir, GUNZIP2.out.gunzip.map{ it[1] } )
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// ANTISMASH_ANTISMASHLITE ( GUNZIP1.out.gunzip, input_db, input_dir, GUNZIP2.out.gunzip.map{ it[1] } )
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}
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// #!/usr/bin/env nextflow
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// nextflow.enable.dsl = 2
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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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// workflow test_antismashlite {
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// input_genome = [
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// [ id:'test' ], // meta map
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// file('/home/jasmin/Downloads/BAN001-megahit.gbk', 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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// input_db = [
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// [],
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// file('/home/jasmin/antismash_db/', checkIfExists: true)
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// ]
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// input_dir = [
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// [],
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// file('/home/jasmin/antismash_dir', checkIfExists: true)
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// ]
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// // input_gff = [
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// // [],
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// // file('/home/jasmin/Downloads/BAN001.gff', 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_genome, input_db, input_dir )
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// }
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