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Some small updates

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This commit is contained in:
Nicolas Vannieuwkerke 2022-04-28 13:31:37 +02:00
parent 9df830f79d
commit 45b4a61a15
3 changed files with 6 additions and 6 deletions
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2
modules/vardictjava/main.nf
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@ -30,7 +30,7 @@ process VARDICTJAVA {
-th $task.cpus \\ -th $task.cpus \\
-N $prefix \\ -N $prefix \\
-G $reference_fasta \\ -G $reference_fasta \\
$regions_of_interest $regions_of_interest \\
| gzip -c > ${prefix}.vcf.gz | gzip -c > ${prefix}.vcf.gz
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml

8
tests/modules/vardictjava/main.nf
View file

@ -6,15 +6,15 @@ include { VARDICTJAVA } from '../../../modules/vardictjava/main.nf'
workflow test_vardictjava { workflow test_vardictjava {
bam_input_ch = Channel.of([ bam_input_ch = Channel.value([
[ id:'test', single_end:false ], // 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)
]) ])
bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true) bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true))
reference = Channel.of([ 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)
]) ])

2
tests/modules/vardictjava/test.yml
View file

@ -4,6 +4,6 @@
- vardictjava - vardictjava
files: files:
- path: output/vardictjava/test.vcf.gz - path: output/vardictjava/test.vcf.gz
md5sum: 2179dcaee6183495b421293f42db11b5 md5sum: 7029066c27ac6f5ef18d660d5741979a
- path: output/vardictjava/versions.yml - path: output/vardictjava/versions.yml
md5sum: aac455b8c9c9194c5fed80e4fd495b96 md5sum: aac455b8c9c9194c5fed80e4fd495b96