nf-core · ramprasadn · Jan 31, 2024 · Jan 31, 2024 · Jan 31, 2024 · Jan 31, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -47,6 +47,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - The split into clincial and research VCFs is now done before ranking the varaints [#485](https://github.com/nf-core/raredisease/pull/485)
 - Installed the nf-core version of ensemblvep/vep module [#482](https://github.com/nf-core/raredisease/pull/482)
 - The filenames of the ranked output VCF files have been changed. See [output.md](docs/output.md#filtering-and-ranking) for more information[#485](https://github.com/nf-core/raredisease/pull/485)
+- Patched cnvnator module so that the processes didn't have to rerun after a failed run [#503](https://github.com/nf-core/raredisease/pull/503).
 
 ### `Fixed`
 

diff --git a/modules.json b/modules.json
@@ -88,7 +88,8 @@
                     "cnvnator/cnvnator": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff"
                     },
                     "cnvnator/convert2vcf": {
                         "branch": "master",

diff --git a/modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff b/modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff
diff --git a/modules/nf-core/cnvnator/cnvnator/main.nf b/modules/nf-core/cnvnator/cnvnator/main.nf
diff --git a/subworkflows/local/variant_calling/call_sv_cnvnator.nf b/subworkflows/local/variant_calling/call_sv_cnvnator.nf
@@ -22,11 +22,11 @@ workflow CALL_SV_CNVNATOR {
     main:
         ch_versions = Channel.empty()
 
-        CNVNATOR_RD ( ch_bam_bai, [[:],[]], [[:],[]], [[:],[]] )
-        CNVNATOR_HIST ( [[:],[],[]], CNVNATOR_RD.out.root, ch_fasta, ch_fai )
-        CNVNATOR_STAT ( [[:],[],[]], CNVNATOR_HIST.out.root, [[:],[]], [[:],[]] )
-        CNVNATOR_PARTITION ( [[:],[],[]], CNVNATOR_STAT.out.root, [[:],[]], [[:],[]] )
-        CNVNATOR_CALL ( [[:],[],[]], CNVNATOR_PARTITION.out.root, [[:],[]], [[:],[]] )
+        CNVNATOR_RD ( ch_bam_bai, [[:],[]], [[:],[]], [[:],[]], "rd" )
+        CNVNATOR_HIST ( [[:],[],[]], CNVNATOR_RD.out.root, ch_fasta, ch_fai, "his" )
+        CNVNATOR_STAT ( [[:],[],[]], CNVNATOR_HIST.out.root, [[:],[]], [[:],[]], "stat" )
+        CNVNATOR_PARTITION ( [[:],[],[]], CNVNATOR_STAT.out.root, [[:],[]], [[:],[]], "partition" )
+        CNVNATOR_CALL ( [[:],[],[]], CNVNATOR_PARTITION.out.root, [[:],[]], [[:],[]], "call" )
         CNVNATOR_CONVERT2VCF (CNVNATOR_CALL.out.tab).vcf
             .collect{it[1]}
             .toList()