fixup! Add support for variant scoring by MIVMIR, GICAM models

lint subworkflows rank_variants

Author: torbjorgen

subworkflows/local/rank_variants/main.nf

@@ -37,18 +37,18 @@ workflow RANK_VARIANTS {
 
         GENMOD_SCORE(ch_score_in, ch_score_config)
 
-        // Run MIVMIR - GICAM scoring (not supported for MT SNVs and SVs)
-        if (rank_with_mivmir_gicam) {
-            GENMOD_SCORE_FOR_GICAM(ch_score_in, ch_genmod_gicam_score_config)
+    // Run MIVMIR - GICAM scoring (not supported for MT SNVs and SVs)
+    if (rank_with_mivmir_gicam) {
+        GENMOD_SCORE_FOR_GICAM(ch_score_in, ch_genmod_gicam_score_config)
 
-            MIVMIR_INFER(GENMOD_SCORE_FOR_GICAM.out.vcf)
+        MIVMIR_INFER(GENMOD_SCORE_FOR_GICAM.out.vcf)
 
-            GICAM_INFER(MIVMIR_INFER.out.vcf)
+        GICAM_INFER(MIVMIR_INFER.out.vcf)
 
-            TABIX_BGZIPTABIX_GICAM(GICAM_INFER.out.vcf)
-        }
+        TABIX_BGZIPTABIX_GICAM(GICAM_INFER.out.vcf)
+    }
 
-        GENMOD_COMPOUND(GENMOD_SCORE.out.vcf)
+    GENMOD_COMPOUND(GENMOD_SCORE.out.vcf)
 
         ch_sort_publish  = channel.empty()
         ch_tabix_publish = channel.empty()
@@ -66,20 +66,26 @@ workflow RANK_VARIANTS {
 
         ch_publish = ch_sort_publish.mix(ch_tabix_publish)
 
-        // Merge Genmod and MIVMIR-GICAM scores
-        if (rank_with_mivmir_gicam) {
-            ch_vcf.join(TABIX_BGZIPTABIX_GICAM.out.gz_index, failOnMismatch: true)
-            .map {meta, vcf_genmod, vcf_gicam, vcf_index_gicam -> return [ meta, vcf_genmod, [], vcf_gicam, vcf_index_gicam, [], [], [] ]}
-            .set {ch_merge_genmod_gicam}
-            BCFTOOLS_MERGE_GENMOD_GICAM(ch_merge_genmod_gicam)
-
-            TABIX_BGZIPTABIX_GENMOD_GICAM(BCFTOOLS_MERGE_GENMOD_GICAM.out.vcf)
-
-            TABIX_BGZIPTABIX_GENMOD_GICAM.out.gz_index.map {meta, vcf, _tbi -> return [meta, vcf]}.set {ch_vcf}
-
-            TABIX_BGZIPTABIX_GENMOD_GICAM.out.gz_index
-                .map { meta, gz, tbi -> ['rank_and_filter/', [meta, gz, tbi]] }.set {ch_publish}
-        }
+    // Merge Genmod and MIVMIR-GICAM scores
+    if (rank_with_mivmir_gicam) {
+        ch_vcf
+            .join(TABIX_BGZIPTABIX_GICAM.out.gz_index, failOnMismatch: true)
+            .map { meta, vcf_genmod, vcf_gicam, vcf_index_gicam ->
+                return [meta, vcf_genmod, [], vcf_gicam, vcf_index_gicam, [], [], []]
+            }
+            .set { ch_merge_genmod_gicam }
+        BCFTOOLS_MERGE_GENMOD_GICAM(ch_merge_genmod_gicam)
+
+        TABIX_BGZIPTABIX_GENMOD_GICAM(BCFTOOLS_MERGE_GENMOD_GICAM.out.vcf)
+
+        TABIX_BGZIPTABIX_GENMOD_GICAM.out.gz_index.map { meta, vcf, _tbi ->
+            return [meta, vcf]
+        }.set { ch_vcf }
+
+        TABIX_BGZIPTABIX_GENMOD_GICAM.out.gz_index
+            .map { meta, gz, tbi -> ['rank_and_filter/', [meta, gz, tbi]] }
+            .set { ch_publish }
+    }
 
     emit:
         publish  = ch_publish   // channel: [ val(destination), val(value) ]