diff --git a/modules/03_metrics.nf b/modules/03_metrics.nf index fe8ff12..af1915b 100644 --- a/modules/03_metrics.nf +++ b/modules/03_metrics.nf @@ -33,15 +33,15 @@ process HS_METRICS { gatk BedToIntervalList \ --INPUT ${params.intervals} \ - --OUTPUT ${params.intervals}.intervals \ + --OUTPUT my.intervals \ --SEQUENCE_DICTIONARY ${bam} gatk CollectHsMetrics \ --java-options '-Xmx${params.metrics_memory} -Djava.io.tmpdir=tmp' \ --INPUT ${bam} \ --OUTPUT ${name}.hs_metrics.txt \ - --TARGET_INTERVALS ${params.intervals}.intervals \ - --BAIT_INTERVALS ${params.intervals}.intervals \ + --TARGET_INTERVALS my.intervals \ + --BAIT_INTERVALS my.intervals \ ${minimum_base_quality} ${minimum_mapping_quality} """ } diff --git a/nextflow.config b/nextflow.config index 9fdfbba..16ebdd1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -46,7 +46,7 @@ process.shell = ['/bin/bash', '-euo', 'pipefail'] cleanup = true -VERSION = '1.7.2' +VERSION = '1.7.3' DOI = 'https://zenodo.org/badge/latestdoi/358400957' manifest {