Merge pull request #573 from nf-core/wes

Turn off workflows irrelevant for WES analysis
nf-core · Jun 24, 2024 · 27fde73 · 27fde73
2 parents 010da06 + 0ccf239
commit 27fde73
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Showing 3 changed files with 51 additions and 36 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Changed`
 
 - `readcount_intervals` parameter is now mandatory for running germlinecnvcaller. [#570](https://github.com/nf-core/raredisease/pull/570)
+- Turn off CNVnator, TIDDIT, SMNCopyNumberCaller, Gens, and Vcf2cytosure for targeted analysis [#573](https://github.com/nf-core/raredisease/pull/573)
 
 ### `Fixed`
 

diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf
@@ -38,10 +38,17 @@ workflow CALL_STRUCTURAL_VARIANTS {
             .collect{it[1]}
             .set{ manta_vcf }
 
-        CALL_SV_TIDDIT (ch_genome_bam_bai, ch_genome_fasta, ch_bwa_index, ch_case_info)
-            .vcf
-            .collect{it[1]}
-            .set { tiddit_vcf }
+        if (params.analysis_type.equals("wgs")) {
+            CALL_SV_TIDDIT (ch_genome_bam_bai, ch_genome_fasta, ch_bwa_index, ch_case_info)
+                .vcf
+                .collect{it[1]}
+                .set { tiddit_vcf }
+
+            CALL_SV_CNVNATOR (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_case_info)
+                .vcf
+                .collect{it[1]}
+                .set { cnvnator_vcf }
+        }
 
         if (!params.skip_germlinecnvcaller) {
             CALL_SV_GERMLINECNVCALLER (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_readcount_intervals, ch_genome_dictionary, ch_ploidy_model, ch_gcnvcaller_model)
@@ -52,28 +59,34 @@ workflow CALL_STRUCTURAL_VARIANTS {
             ch_versions = ch_versions.mix(CALL_SV_GERMLINECNVCALLER.out.versions)
         }
 
-        CALL_SV_CNVNATOR (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_case_info)
-            .vcf
-            .collect{it[1]}
-            .set { cnvnator_vcf }
-
         if (params.analysis_type.equals("wgs") || params.run_mt_for_wes) {
             CALL_SV_MT (ch_mt_bam_bai, ch_genome_fasta)
             ch_versions = ch_versions.mix(CALL_SV_MT.out.versions)
         }
 
         //merge
         if (params.skip_germlinecnvcaller) {
+            if (params.analysis_type.equals("wgs")) {
+                tiddit_vcf
+                    .combine(manta_vcf)
+                    .combine(cnvnator_vcf)
+                    .toList()
+                    .set { vcf_list }
+            } else {
+                manta_vcf
+                    .toList()
+                    .set { vcf_list }
+            }
+        } else if (params.analysis_type.equals("wgs")){
             tiddit_vcf
                 .combine(manta_vcf)
+                .combine(gcnvcaller_vcf)
                 .combine(cnvnator_vcf)
                 .toList()
                 .set { vcf_list }
         } else {
-            tiddit_vcf
-                .combine(manta_vcf)
+            manta_vcf
                 .combine(gcnvcaller_vcf)
-                .combine(cnvnator_vcf)
                 .toList()
                 .set { vcf_list }
         }

diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf
@@ -695,28 +695,29 @@ workflow RAREDISEASE {
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-    RENAME_BAM_FOR_SMNCALLER(ch_mapped.genome_marked_bam, "bam").output
-        .collect{it}
-        .toList()
-        .set { ch_bam_list }
-
-    RENAME_BAI_FOR_SMNCALLER(ch_mapped.genome_marked_bai, "bam.bai").output
-        .collect{it}
-        .toList()
-        .set { ch_bai_list }
-
-    ch_case_info
-        .combine(ch_bam_list)
-        .combine(ch_bai_list)
-        .set { ch_bams_bais }
-
-    SMNCOPYNUMBERCALLER (
-        ch_bams_bais
-    )
-    ch_versions = ch_versions.mix(RENAME_BAM_FOR_SMNCALLER.out.versions)
-    ch_versions = ch_versions.mix(RENAME_BAI_FOR_SMNCALLER.out.versions)
-    ch_versions = ch_versions.mix(SMNCOPYNUMBERCALLER.out.versions)
-
+    if ( params.analysis_type.equals("wgs") ) {
+        RENAME_BAM_FOR_SMNCALLER(ch_mapped.genome_marked_bam, "bam").output
+            .collect{it}
+            .toList()
+            .set { ch_bam_list }
+
+        RENAME_BAI_FOR_SMNCALLER(ch_mapped.genome_marked_bai, "bam.bai").output
+            .collect{it}
+            .toList()
+            .set { ch_bai_list }
+
+        ch_case_info
+            .combine(ch_bam_list)
+            .combine(ch_bai_list)
+            .set { ch_bams_bais }
+
+        SMNCOPYNUMBERCALLER (
+            ch_bams_bais
+        )
+        ch_versions = ch_versions.mix(RENAME_BAM_FOR_SMNCALLER.out.versions)
+        ch_versions = ch_versions.mix(RENAME_BAI_FOR_SMNCALLER.out.versions)
+        ch_versions = ch_versions.mix(SMNCOPYNUMBERCALLER.out.versions)
+    }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     PEDDY
@@ -735,7 +736,7 @@ workflow RAREDISEASE {
     Generate CGH files from sequencing data
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
-    if ( !params.skip_vcf2cytosure && params.analysis_type != "wes" ) {
+    if ( !params.skip_vcf2cytosure && params.analysis_type.equals("wgs") ) {
         GENERATE_CYTOSURE_FILES (
             ch_sv_annotate.vcf_ann,
             ch_sv_annotate.tbi,
@@ -751,7 +752,7 @@ workflow RAREDISEASE {
     GENS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
-    if ( !params.skip_gens && params.analysis_type != "wes" ) {
+    if ( !params.skip_gens && params.analysis_type.equals("wgs") ) {
         GENS (
             ch_mapped.genome_bam_bai,
             CALL_SNV.out.genome_gvcf,