Merge branch 'update/pipeline_template_2.10' of github.com:mskcc/fort…

…e into update/pipeline_template_2.10
mskcc · Nov 20, 2023 · 5d12994 · 5d12994
2 parents a6ed309 + 6d7c413
commit 5d12994
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diff --git a/conf/modules.config b/conf/modules.config
@@ -180,13 +180,6 @@ process {
             'mm39'
     }
 
-    withName: FUSIONREPORT_DOWNLOAD {
-        ext.when = ! params.skip_fusion_report
-        secret = ["COSMIC_PASSWD"]
-        storeDir = { "${params.reference_base}/fusionreport" }
-        ext.args = "--cosmic_usr ${params.cosmic_usr} --cosmic_passwd \$COSMIC_PASSWD"
-    }
-
     withName: MERGE_CFF {
         publishDir = [
             enabled: false

diff --git a/modules/local/fusionreport/download/main.nf b/modules/local/fusionreport/download/main.nf
diff --git a/modules/local/fusionreport/download/meta.yml b/modules/local/fusionreport/download/meta.yml
diff --git a/modules/local/fusionreport/run/main.nf b/modules/local/fusionreport/run/main.nf
diff --git a/modules/local/fusionreport/run/meta.yml b/modules/local/fusionreport/run/meta.yml
diff --git a/nextflow.config b/nextflow.config
@@ -34,7 +34,6 @@ params {
     run_oncokb_fusionannotator = false
     cosmic_usr                 = null
     fusion_report_cutoff       = 1
-    skip_fusion_report         = false
     fusion_tool_cutoff         = 1
 
     // QC