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Merge branch 'master' into add_compression_to_bam2fq

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Lauri Mesilaakso 2022-05-03 17:03:02 +03:00 committed by GitHub
commit 12f79c2101
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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' }"
input:
tuple val(meta), path(bam), path(bai)
path(bed)
tuple val(meta), path(bam), path(bai), path(bed)
tuple path(fasta), path(fasta_fai)
output:

7
tests/modules/vardictjava/main.nf
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@ -9,15 +9,14 @@ workflow test_vardictjava {
bam_input_ch = Channel.value([
[ 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_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([
file(params.test_data['homo_sapiens']['genome']['genome_fasta'], 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 )
}