diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf index 855784db..e1098b22 100644 --- a/modules/vardictjava/main.nf +++ b/modules/vardictjava/main.nf @@ -8,7 +8,8 @@ process VARDICTJAVA { 'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }" input: - tuple val(meta), path(bam), path(regions_of_interest) + tuple val(meta), path(bam) + path(regions_of_interest) path(reference_fasta) output: @@ -23,14 +24,11 @@ process VARDICTJAVA { def prefix = task.ext.prefix ?: "${meta.id}" """ - head -n 20 $reference_fasta - cat $reference_fasta | wc -l - vardict-java \\ $args \\ -b $bam \\ -th $task.cpus \\ - -n $prefix \\ + -N $prefix \\ -G $reference_fasta \\ $regions_of_interest \\ > ${prefix}.vcf diff --git a/tests/modules/vardictjava/main.nf b/tests/modules/vardictjava/main.nf index 7511b529..647c8bba 100644 --- a/tests/modules/vardictjava/main.nf +++ b/tests/modules/vardictjava/main.nf @@ -6,14 +6,14 @@ include { VARDICTJAVA } from '../../../modules/vardictjava/main.nf' workflow test_vardictjava { - input = [ + bam_input_ch = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] + ]) - VARDICTJAVA ( - input, - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) - ) + bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + + VARDICTJAVA ( bam_input_ch, bed, fasta ) }