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Update bedtools modules with config logic (#369)

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Harshil Patel 2021-03-24 14:14:19 +00:00 committed by GitHub
parent 83a500e6b0
commit c7155d023e
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8 changed files with 16 additions and 16 deletions
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4
tests/software/bedtools/complement/main.nf
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@ -6,9 +6,9 @@ include { BEDTOOLS_COMPLEMENT } from '../../../../software/bedtools/complement/m
workflow test_bedtools_complement {
input = [ [ id:'test'],
file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
]
sizes = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.sizes", checkIfExists: true)
sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
BEDTOOLS_COMPLEMENT ( input, sizes )
}

2
tests/software/bedtools/genomecov/main.nf
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@ -6,7 +6,7 @@ include { BEDTOOLS_GENOMECOV } from '../../../../software/bedtools/genomecov/mai
workflow test_bedtools_genomecov {
input = [ [ id:'test'],
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.bam", checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BEDTOOLS_GENOMECOV ( input )

6
tests/software/bedtools/getfasta/main.nf
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@ -5,8 +5,8 @@ nextflow.enable.dsl = 2
include { BEDTOOLS_GETFASTA } from '../../../../software/bedtools/getfasta/main.nf' addParams( options: [:] )
workflow test_bedtools_getfasta {
bed = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) ]
fasta = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BEDTOOLS_GETFASTA ( bed, fasta )
}

4
tests/software/bedtools/intersect/main.nf
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@ -6,8 +6,8 @@ include { BEDTOOLS_INTERSECT } from '../../../../software/bedtools/intersect/mai
workflow test_bedtools_intersect {
input = [ [ id:'test' ],
file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test2.bed", checkIfExists: true)
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)
]
BEDTOOLS_INTERSECT ( input )

6
tests/software/bedtools/maskfasta/main.nf
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@ -6,9 +6,9 @@ include { BEDTOOLS_MASKFASTA } from '../../../../software/bedtools/maskfasta/mai
workflow test_bedtools_maskfasta {
bed = [ [ id:'test'],
file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
]
fasta = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BEDTOOLS_MASKFASTA ( bed, fasta )
}

2
tests/software/bedtools/merge/main.nf
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@ -6,7 +6,7 @@ include { BEDTOOLS_MERGE } from '../../../../software/bedtools/merge/main.nf' ad
workflow test_bedtools_merge {
input = [ [ id:'test'],
file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
]
BEDTOOLS_MERGE ( input )

6
tests/software/bedtools/slop/main.nf
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@ -6,10 +6,10 @@ include { BEDTOOLS_SLOP } from '../../../../software/bedtools/slop/main.nf' addP
workflow test_bedtools_slop {
input = [ [ id:'test'],
file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
]
sizes = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.sizes", checkIfExists: true)
sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
BEDTOOLS_SLOP ( input, sizes )
}

2
tests/software/bedtools/sort/main.nf
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@ -6,7 +6,7 @@ include { BEDTOOLS_SORT } from '../../../../software/bedtools/sort/main.nf' addP
workflow test_bedtools_sort {
input = [ [ id:'test'],
file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
]
BEDTOOLS_SORT ( input )