Merge pull request #837 from nf-core/sanitycheckxtra

Fix issues in call_sv_MT & extend vcfanno sanity check

Author: ramprasadn

CHANGELOG.md

@@ -75,6 +75,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fixed CADD annotation to support chr prefix [#745](https://github.com/nf-core/raredisease/pull/745)
 - Fixed mismatch between VCF and ROH calls when analysing multiple samples [#755](https://github.com/nf-core/raredisease/pull/755)
 - Fixed pipeline to run variant calling even with bait_padding set to 0 [#757](https://github.com/nf-core/raredisease/pull/757)
+- Fixed runtime errors in `call_sv_MT` and `call_structural_variants` when MitoSAlt produces no structural variant calls [#837](https://github.com/nf-core/raredisease/pull/837)
+- Fixed vcfanno sanity check map closure to handle `ch_vcfanno_resources` emitting a list of paths [#837](https://github.com/nf-core/raredisease/pull/837)
 
 ### Parameters
 

nextflow_schema.json

@@ -620,7 +620,7 @@
                     "fa_icon": "fas fa-forward",
                     "description": "Disable specified tools.",
                     "help_text": "Multiple tools can be specified, separated by commas.",
-                    "pattern": "^((fastp|gens|germlinecnvcaller|peddy|smncopynumbercaller|vcf2cytosure|fastqc|ngsbits)?,?)*(?<!,)$"
+                    "pattern": "^((fastp|gens|germlinecnvcaller|peddy|smncopynumbercaller|vcf2cytosure|fastqc|ngsbits|mitosalt)?,?)*(?<!,)$"
                 }
             }
         },

subworkflows/local/call_structural_variants/main.nf

@@ -141,9 +141,10 @@ workflow CALL_STRUCTURAL_VARIANTS {
             ch_merged_tbi = TABIX_TABIX.out.index
 
         } else {
-            // For mito-only analysis, use mitosalt_vcf directly
-            TABIX_TABIX (ch_saltshaker_vcf)
-            ch_merged_svs = ch_saltshaker_vcf
+            // For mito-only analysis, use saltshaker_vcf with meta directly (ch_saltshaker_vcf
+            // holds collected paths only, ch_sv_mt_out.saltshaker_vcf holds [meta, vcf] tuples)
+            TABIX_TABIX (ch_sv_mt_out.saltshaker_vcf)
+            ch_merged_svs = ch_sv_mt_out.saltshaker_vcf
             ch_merged_tbi = TABIX_TABIX.out.index
         }
 

subworkflows/local/call_sv_MT/main.nf

@@ -40,6 +40,7 @@ workflow CALL_SV_MT {
         val_mitosalt_heteroplasmy_limit       // string: [mandatory] mitosalt_heteroplasmy_limit
 
     main:
+        ch_saltshaker_html  = channel.empty()
         ch_saltshaker_txt   = channel.empty()
         ch_saltshaker_vcf   = channel.empty()
         ch_saltshaker_plot  = channel.empty()
@@ -131,16 +132,17 @@ workflow CALL_SV_MT {
             )
             ch_saltshaker_plot = SALTSHAKER_PLOT.out.plot
 
+            // Only merge if Saltshaker produced VCFs; filter on the flat list before wrapping so
+            // combine never sees an empty-spread issue (combining case_info with [[]] would produce
+            // a 1-element channel item that breaks 2-param destructuring closures downstream).
             SALTSHAKER_CLASSIFY.out.vcf
                 .collect{ _meta, vcf -> vcf }
-                .toList()
+                .filter{ !it.isEmpty() }
+                .map{ vcf_list -> [vcf_list] }
                 .set { ch_vcf_file_list }
 
-            // Saltshaker only runs if there are mitosalt calls, so we only merge in that case (ie vcfs
-            // exist, combined channel has two elements) to avoid a merge error
             ch_case_info
                 .combine(ch_vcf_file_list)
-                .filter{ it -> it.size() == 2}
                 .set { ch_merge_input_vcfs }
 
             SVDB_MERGE ( ch_merge_input_vcfs, [], true ).vcf

workflows/raredisease.nf

@@ -446,7 +446,7 @@ workflow RAREDISEASE {
         if (val_run_vcfanno_db_sanity_check && (!skip_snv_annotation || (!skip_mt_annotation && (val_run_mt_for_wes || val_analysis_type.matches("wgs|mito"))))) {
             ch_vcfanno_resources
                 .combine(ch_vcfanno_extra)
-                .map { resources, extra -> [resources, extra].flatten() }
+                .map { files -> files.flatten() }
                 .set { ch_all_vcfanno_dbs }
             SANITY_CHECK_VCFANNO_DATABASES (ch_vcfanno_toml, ch_all_vcfanno_dbs)
             ch_vcfanno_toml_final = SANITY_CHECK_VCFANNO_DATABASES.out.toml