merge upstream/dev

Author: FriederikeHanssen

conf/modules.config

@@ -1105,7 +1105,7 @@ process{
             publishDir       = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/variant_calling/tiddit/${meta.id}/" },
-                pattern: "*{vcf,vcf.gz}"
+                pattern: "*vcf.gz"
             ]
         }
     }

modules.json

@@ -223,7 +223,7 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "svdb/merge": {
-                "git_sha": "313d76e00525c8e975dabce0c34973fd53c3f4dd"
+                "git_sha": "6b011dd14821385c282e030c6d993d2116aed23f"
             },
             "tabix/bgziptabix": {
                 "git_sha": "9dbaffff88013bc21460a989cde7a5aa172c2e0b"

modules/nf-core/modules/svdb/merge/main.nf

@@ -989,7 +989,7 @@
     - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.ploidies.tab
     - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.tumor.vcf.gz
     - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.tumor.vcf.gz.tbi
-    - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit_sv_merge.vcf
+    - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit_sv_merge.vcf.gz
 - name: Run variant calling on germline sample with tiddit
   command: nextflow run main.nf -profile test,tools_germline,docker --tools tiddit
   tags: