Fix unique lanes for freebayes, groupKey, add new indices, copy meta maps

CHANGELOG.md

@@ -73,6 +73,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#513](https://github.com/nf-core/sarek/pull/513), [#527](https://github.com/nf-core/sarek/pull/527) - CNV is back
 - [#529](https://github.com/nf-core/sarek/pull/529) - Do not save `versions.yml` files
 - [#524](https://github.com/nf-core/sarek/pull/524) - Fix intervals usage by counting the actual list of scatter/gather files produced and not overall number of intervals
+- [#549](https://github.com/nf-core/sarek/pull/549) - Fix unique lanes required for Freebayes: issue [#311](https://github.com/nf-core/sarek/issues/311), replaces `meta.clone()` with actual copy of map to avoid issues with https://nfcore.slack.com/archives/C027CM7P08M/p1644241819942339
 
 ### Deprecated
 

conf/igenomes.config

@@ -38,7 +38,7 @@ params {
             ac_loci_gc            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci.gc"
             bwa                   = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/"
             bwamem2               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/"
-            hashmap               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/dragmap/"
+            dragmap               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/dragmap/"
             chr_dir               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes"
             dbsnp                 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz"
             dbsnp_tbi             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi"
@@ -51,6 +51,8 @@ params {
             known_indels          = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
             known_indels_tbi      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
             mappability           = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem"
+            pon                   = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz"
+            pon_tbi               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi"
             snpeff_db             = 'GRCh38.99'
             snpeff_genome         = 'GRCh38'
             vep_cache_version     = 104

conf/modules.config

@@ -475,13 +475,9 @@ process{
         // For unknown reasons, CONCAT_VCF sometimes fails with SIGPIPE
         // (exit code 141). Rerunning the process will usually work.
         errorStrategy   = {task.exitStatus == 141 ? 'retry' : 'terminate'}
-        ext.args         = { params.no_intervals ?  "-n" : "" }
-    }
-    withName : 'TABIX_VC_.*' {
-        ext.when         = { params.no_intervals }
+        ext.args         = { params.no_intervals ?  "-n" : "" } //Why ConcatVCF is never run when no_intervals is set..
     }
     withName : 'BGZIP_VC_.*' {
-        ext.when         = { !params.no_intervals }
         publishDir       = [
             enabled: false
         ]
@@ -525,15 +521,23 @@ process{
         ]
     }
     withName: 'FREEBAYES' {
+        ext.prefix       = {"${meta.id}.freebayes"} //To make sure no naming conflicts ensue with module BCFTOOLS_SORT & the naming being correct in the output folder
         ext.args         = '--min-alternate-fraction 0.1 --min-mapping-quality 1'
         ext.when         = { params.tools && params.tools.contains('freebayes') }
+        publishDir       = [
+            enabled: false
+        ]
+    }
+
+    withName: 'BCFTOOLS_SORT' {
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" },
             pattern: "*vcf.gz",
             saveAs: { meta.num_intervals > 1 ? null : it }
         ]
     }
+
     withName : 'TABIX_VC_FREEBAYES' {
         publishDir       = [
             mode: params.publish_dir_mode,
@@ -900,6 +904,18 @@ process{
             }
     }
 
+    //FREEBAYES
+    withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_FREEBAYES_SOMATIC:FREEBAYES' {
+        ext.args = "--pooled-continuous \
+                    --pooled-discrete \
+                    --genotype-qualities \
+                    --report-genotype-likelihood-max \
+                    --allele-balance-priors-off \
+                    --min-alternate-fraction 0.03 \
+                    --min-repeat-entropy 1 \
+                    --min-alternate-count 2 "
+    }
+
     //MANTA
     withName: 'CONCAT_MANTA_SOMATIC' {
         ext.prefix       = {"${meta.id}.somatic_sv"}