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Split the bed file into a seperate input

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This commit is contained in:
Nicolas Vannieuwkerke 2022-04-28 09:18:15 +02:00
parent 1fd4719e9d
commit db43095b1a
2 changed files with 10 additions and 12 deletions
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8
modules/vardictjava/main.nf
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@ -8,7 +8,8 @@ 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(regions_of_interest) tuple val(meta), path(bam)
path(regions_of_interest)
path(reference_fasta) path(reference_fasta)
output: output:
@ -23,14 +24,11 @@ process VARDICTJAVA {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
head -n 20 $reference_fasta
cat $reference_fasta | wc -l
vardict-java \\ vardict-java \\
$args \\ $args \\
-b $bam \\ -b $bam \\
-th $task.cpus \\ -th $task.cpus \\
-n $prefix \\ -N $prefix \\
-G $reference_fasta \\ -G $reference_fasta \\
$regions_of_interest \\ $regions_of_interest \\
> ${prefix}.vcf > ${prefix}.vcf

14
tests/modules/vardictjava/main.nf
View file

@ -6,14 +6,14 @@ include { VARDICTJAVA } from '../../../modules/vardictjava/main.nf'
workflow test_vardictjava { workflow test_vardictjava {
input = [ bam_input_ch = Channel.of([
[ id:'test', single_end:false ], // meta map [ id:'test', single_end:false ], // 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)
] ])
VARDICTJAVA ( bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
input,
file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true), fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
) VARDICTJAVA ( bam_input_ch, bed, fasta )
} }