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Update antismashlite module main.nf

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This commit is contained in:
jasmezz 2022-04-26 17:15:41 +02:00
parent 1acde9a7a1
commit cc05006dbb
1 changed files with 22 additions and 22 deletions
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44
tests/modules/antismash/antismashlite/main.nf
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@ -10,32 +10,32 @@ include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/anti
include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/antismash/antismashlite/main.nf'
include { PROKKA } from '../../../modules/prokka/main.nf'
// workflow test_antismashlite {
// input = [
// [ id:'test' ], // meta map
// file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true) ]
workflow test_antismashlite {
input = [
[ id:'test' ], // meta map
file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true) ]
// input_antismash_db1 = [
// [],
// file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
// ]
input_antismash_db1 = [
[],
file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
]
// input_antismash_db2 = [
// [],
// file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
// ]
input_antismash_db2 = [
[],
file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
]
// input_antismash_db3 = [
// [],
// file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
// ]
input_antismash_db3 = [
[],
file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
]
// UNTAR1 ( input_antismash_db1 )
// UNTAR2 ( input_antismash_db2 )
// UNTAR3 ( input_antismash_db3 )
// ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] }, UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
// ANTISMASH_ANTISMASHLITE ( input, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, UNTAR1.out.untar.map{ it[1] }, UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
//}
UNTAR1 ( input_antismash_db1 )
UNTAR2 ( input_antismash_db2 )
UNTAR3 ( input_antismash_db3 )
ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] }, UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
ANTISMASH_ANTISMASHLITE ( input, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, UNTAR1.out.untar.map{ it[1] }, UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
}
workflow test_prokka_antismashlite {
input_gunzip = [ [ id:'test' ], // meta map