Don't pass in intervals file to freec

CHANGELOG.md

@@ -58,6 +58,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas
 - [#1203](https://github.com/nf-core/sarek/pull/1203) - Fix issue with Singularity containers on test profiles
 - [#1204](https://github.com/nf-core/sarek/pull/1204) - Fix issue with nf-validation: lane can be a requirement of bam too now
 - [#1205](https://github.com/nf-core/sarek/pull/1205) - Less tests triggered
+- [#](https://github.com/nf-core/sarek/pull/) - Don't pass in intervals file to ControlFREEC for WGS analysis
 
 ### Dependencies
 

subworkflows/local/bam_variant_calling_somatic_all/main.nf

@@ -41,6 +41,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
     gc_file                       // channel: [optional]  ascat gc content file
     rt_file                       // channel: [optional]  ascat rt file
     joint_mutect2                 // boolean: [mandatory] [default: false] run mutect2 in joint mode
+    wes                           // boolean: [mandatory] [default: false] whether targeted data is processed
 
     main:
     versions          = Channel.empty()
@@ -94,6 +95,8 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
 
         length_file = cf_chrom_len ?: fasta_fai
 
+        intervals_controlfreec = wes ? intervals_bed_combined : []
+
         BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC(
             mpileup_pair,
             fasta,
@@ -102,7 +105,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
             dbsnp_tbi,
             chr_files,
             mappability,
-            intervals_bed_combined
+            intervals_controlfreec
         )
 
         versions = versions.mix(MPILEUP_NORMAL.out.versions)

subworkflows/local/bam_variant_calling_tumor_only_all/main.nf

@@ -61,7 +61,8 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
 
     // CONTROLFREEC (depends on MPILEUP)
     if (tools.split(',').contains('controlfreec')) {
-        length_file = cf_chrom_len ?: fasta_fai
+        length_file            = cf_chrom_len ?: fasta_fai
+        intervals_controlfreec = wes ? intervals_bed_combined : []
 
         BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC(
             // Remap channel to match module/subworkflow
@@ -72,7 +73,7 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
             dbsnp_tbi,
             chr_files,
             mappability,
-            intervals_bed_combined
+            intervals_controlfreec
         )
 
         versions = versions.mix(BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC.out.versions)

workflows/sarek.nf

@@ -1146,7 +1146,8 @@ workflow SAREK {
             mappability,
             pon,
             pon_tbi,
-            params.joint_mutect2
+            params.joint_mutect2,
+            params.wes
         )
 
         // PAIR VARIANT CALLING
@@ -1175,7 +1176,8 @@ workflow SAREK {
             loci_files,
             gc_file,
             rt_file,
-            params.joint_mutect2
+            params.joint_mutect2,
+            params.wes
         )
 
         // POST VARIANTCALLING