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Update restructured paths (#380)

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* dsh filterbed path updated

* dsh splitbed path updated

* adapterremoval path updated
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pericsson 2021-03-24 19:26:54 +01:00 committed by GitHub
parent 62775ea203
commit 1e4fa57139
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3 changed files with 7 additions and 7 deletions
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10
tests/software/adapterremoval/main.nf
View file

@ -6,7 +6,7 @@ include { ADAPTERREMOVAL } from '../../../software/adapterremoval/main.nf' addPa
workflow test_adapterremoval_single_end {
input = [ [ id:'test', single_end:true, collapse:false ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
]
ADAPTERREMOVAL ( input )
@ -14,8 +14,8 @@ workflow test_adapterremoval_single_end {
workflow test_adapterremoval_paired_end {
input = [ [ id:'test', single_end:false, collapse:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
ADAPTERREMOVAL ( input )
@ -23,8 +23,8 @@ workflow test_adapterremoval_paired_end {
workflow test_adapterremoval_paired_end_collapse {
input = [ [ id:'test', single_end:false, collapse:true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
ADAPTERREMOVAL ( input )

2
tests/software/dsh/filterbed/main.nf
View file

@ -6,7 +6,7 @@ include { DSH_FILTERBED } from '../../../../software/dsh/filterbed/main.nf' addP
workflow test_dsh_filterbed {
input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
]
DSH_FILTERBED ( input )

2
tests/software/dsh/splitbed/main.nf
View file

@ -6,7 +6,7 @@ include { DSH_SPLITBED } from '../../../../software/dsh/splitbed/main.nf' addPar
workflow test_dsh_splitbed {
input = [ [ id:'test' ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
]
DSH_SPLITBED ( input )