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Another update to delly/call (#2011)

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small update
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nvnieuwk 2022-09-05 16:06:56 +02:00 committed by GitHub
parent 8bc5236371
commit 30102f3b20
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2 changed files with 7 additions and 8 deletions
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3
modules/delly/call/main.nf
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@ -8,8 +8,7 @@ process DELLY_CALL {
'quay.io/biocontainers/delly:1.1.3--h358d541_0' }" 'quay.io/biocontainers/delly:1.1.3--h358d541_0' }"
input: input:
tuple val(meta), path(input), path(input_index) tuple val(meta), path(input), path(input_index), path(exclude_bed)
path exclude_bed
path fasta path fasta
path fai path fai

12
tests/modules/delly/call/main.nf
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@ -8,37 +8,37 @@ workflow test_delly_call_bam {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
[]
] ]
exclude_regions = []
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
DELLY_CALL ( input, exclude_regions, fasta, fai ) DELLY_CALL ( input, fasta, fai )
} }
workflow test_delly_call_cram { workflow test_delly_call_cram {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
[]
] ]
exclude_regions = []
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
DELLY_CALL ( input, exclude_regions, fasta, fai ) DELLY_CALL ( input, fasta, fai )
} }
workflow test_delly_call_exclude_regions { workflow test_delly_call_exclude_regions {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
] ]
exclude_regions = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
DELLY_CALL ( input, exclude_regions, fasta, fai ) DELLY_CALL ( input, fasta, fai )
} }