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Moved the BED file to the main tuple

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This commit is contained in:
Nicolas Vannieuwkerke 2022-05-03 15:31:05 +02:00
parent 1baf143607
commit 96d4a31cc1
2 changed files with 4 additions and 6 deletions
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3
modules/vardictjava/main.nf
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@ -10,8 +10,7 @@ process VARDICTJAVA {
'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }" 'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam), path(bai) tuple val(meta), path(bam), path(bai), path(bed)
path(bed)
tuple path(fasta), path(fasta_fai) tuple path(fasta), path(fasta_fai)
output: output:

7
tests/modules/vardictjava/main.nf
View file

@ -9,15 +9,14 @@ workflow test_vardictjava {
bam_input_ch = Channel.value([ bam_input_ch = Channel.value([
[ id:'test' ], // meta map [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
]) ])
bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true))
reference = Channel.value([ reference = Channel.value([
file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true), file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
]) ])
VARDICTJAVA ( bam_input_ch, bed, reference ) VARDICTJAVA ( bam_input_ch, reference )
} }