make index available to VQSR

TRON-Bioinformatics · Dec 12, 2021 · 75f0266 · 75f0266
1 parent c4ad9a4
commit 75f0266
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/modules/02_vqsr.nf b/modules/02_vqsr.nf
@@ -45,7 +45,8 @@ process VARIANT_RECALIBRATOR {
     tuple val(name), file(vcf)
 
     output:
-    tuple val("${name}"), file(vcf), file("output.tranches"), file("${name}.recalibrated.vcf"), emit: recalibration
+    tuple val("${name}"), file(vcf), file("output.tranches"), file("${name}.recalibrated.vcf"),
+        file("${name}.recalibrated.vcf.idx"), emit: recalibration
 
     """
     gatk --java-options '-Xmx${params.memory_filter}' VariantRecalibrator \
@@ -70,7 +71,7 @@ process VQSR {
     conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
 
     input:
-    tuple val(name), file(vcf), file(tranches_file), file(recalibration_file)
+    tuple val(name), file(vcf), file(tranches_file), file(recalibration_file), file(index)
 
     output:
     tuple val("${name}"), file("${name}.hc.vcf"), emit: final_vcfs

diff --git a/nextflow.config b/nextflow.config
@@ -33,7 +33,7 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
-VERSION = '0.1.3'
+VERSION = '0.1.4'
 DOI = 'bla'
 
 manifest {