Merge pull request #4 from TRON-Bioinformatics/fix-intervals-issue

avoid creating a global intervals file over and over again with a ris…
TRON-Bioinformatics · Dec 9, 2021 · 055e84e · 055e84e
2 parents f3f480c + e7d9e7f
commit 055e84e
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 4 deletions.
diff --git 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
@@ -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 {