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Add test workflows

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This commit is contained in:
Thomas A. Christensen II 2022-07-18 10:02:33 -05:00
parent 8c1b2a34f2
commit 3f0523ef88
Signed by: millironx
GPG key ID: 139C07724802BC5D
1 changed files with 39 additions and 4 deletions
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41
tests/modules/emboss/seqret/main.nf
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@ -3,13 +3,48 @@
nextflow.enable.dsl = 2
include { EMBOSS_SEQRET } from '../../../../modules/emboss/seqret/main.nf'
include { GUNZIP } from '../../../modules/gunzip/main.nf'
workflow test_emboss_seqret {
workflow test_emboss_seqret_gb2embl {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
]
EMBOSS_SEQRET ( input )
GUNZIP ( input )
EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'embl' )
}
workflow test_emboss_seqret_gb2gff {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
]
GUNZIP ( input )
EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'gff' )
}
workflow test_emboss_seqret_gb2pir {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
]
GUNZIP ( input )
EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'pir' )
}
workflow test_emboss_seqret_gb2fasta {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
]
GUNZIP ( input )
EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'fasta' )
}