fix: msisensor output directory

nf-core · Oct 22, 2020 · dc85282 · dc85282
1 parent 3517511
commit dc85282
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diff --git a/conf/modules.config b/conf/modules.config
@@ -159,6 +159,7 @@ params {
         'msisensor_msi' {
             publish_by_id    = "true"
             publish_dir      = "variant_calling"
+            publish_files    = ['list':'msisensor']
         }
         'strelka_somatic' {
             publish_by_id    = "true"

diff --git a/main.nf b/main.nf
@@ -328,6 +328,7 @@ include { GERMLINE_VARIANT_CALLING } from './modules/local/subworkflow/germline_
 // include { TUMOR_VARIANT_CALLING } from './modules/local/subworkflow/tumor_variant_calling' addParams(
 // )
 include { PAIR_VARIANT_CALLING } from './modules/local/subworkflow/pair_variant_calling' addParams(
+    msisensor_msi_options:           modules['msisensor_msi'],
     manta_options:                   modules['manta_somatic'],
     strelka_options:                 modules['strelka_somatic']
 )