Merge pull request #788 from nf-core/gatk-java-fix

Fix GATK memory specs and MVA add vcf files

Author: jfy133

CHANGELOG.md

@@ -21,6 +21,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#612](https://github.com/nf-core/eager/issues/612) Updated BAM trimming defaults to 0 to ensure no unwanted trimming when mixing half-UDG with no-UDG (thanks to @scarlhoff)
 - [#722](https://github.com/nf-core/eager/issues/722) Updated BWA mapping mapping parameters to latest recommendations - primarily alnn back to 0.01 and alno to 2 as per Oliva et al. 2021 (10.1093/bib/bbab076)
 - Updated workflow diagrams to reflect latest functionality
+- [#787](https://github.com/nf-core/eager/issues/787) Adds memory specification flags for the GATK UnifiedGenotyper and HaplotyperCaller steps (thanks to @nylander)
+- Fixed issue where MultiVCFAnalyzer would not pick up newly generated VCF files, when specifying additional VCF files.
 
 ### `Dependencies`
 

README.md

@@ -169,6 +169,7 @@ Those who have provided conceptual guidance, suggestions, bug reports etc.
 * [Ido Bar](https://github.com/IdoBar)
 * [Irina Velsko](https://github.com/ivelsko)
 * [Işın Altınkaya](https://github.com/isinaltinkaya)
+* [Johan Nylander](https://github.com/nylander)
 * [Katerine Eaton](https://github.com/ktmeaton)
 * [Katrin Nägele](https://github.com/KathrinNaegele)
 * [Luc Venturini](https://github.com/lucventurini)

main.nf

@@ -2355,9 +2355,9 @@ process genotyping_ug {
   if (!params.gatk_dbsnp)
     """
     samtools index -b ${bam}
-    gatk3 -T RealignerTargetCreator -R ${fasta} -I ${bam} -nt ${task.cpus} -o ${samplename}.intervals ${defaultbasequalities}
-    gatk3 -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${samplename}.intervals -o ${samplename}.realign.bam ${defaultbasequalities}
-    gatk3 -T UnifiedGenotyper -R ${fasta} -I ${samplename}.realign.bam -o ${samplename}.unifiedgenotyper.vcf -nt ${task.cpus} --genotype_likelihoods_model ${params.gatk_ug_genotype_model} -stand_call_conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} -dcov ${params.gatk_downsample} --output_mode ${params.gatk_ug_out_mode} ${defaultbasequalities}
+    gatk3 -Xmx${task.memory.toGiga()}g -T RealignerTargetCreator -R ${fasta} -I ${bam} -nt ${task.cpus} -o ${samplename}.intervals ${defaultbasequalities}
+    gatk3 -Xmx${task.memory.toGiga()}g -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${samplename}.intervals -o ${samplename}.realign.bam ${defaultbasequalities}
+    gatk3 -Xmx${task.memory.toGiga()}g -T UnifiedGenotyper -R ${fasta} -I ${samplename}.realign.bam -o ${samplename}.unifiedgenotyper.vcf -nt ${task.cpus} --genotype_likelihoods_model ${params.gatk_ug_genotype_model} -stand_call_conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} -dcov ${params.gatk_downsample} --output_mode ${params.gatk_ug_out_mode} ${defaultbasequalities}
     
     $keep_realign
     
@@ -2366,9 +2366,9 @@ process genotyping_ug {
   else if (params.gatk_dbsnp)
     """
     samtools index ${bam}
-    gatk3 -T RealignerTargetCreator -R ${fasta} -I ${bam} -nt ${task.cpus} -o ${samplename}.intervals ${defaultbasequalities}
-    gatk3 -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${samplenane}.intervals -o ${samplename}.realign.bam ${defaultbasequalities}
-    gatk3 -T UnifiedGenotyper -R ${fasta} -I ${samplename}.realign.bam -o ${samplename}.unifiedgenotyper.vcf -nt ${task.cpus} --dbsnp ${params.gatk_dbsnp} --genotype_likelihoods_model ${params.gatk_ug_genotype_model} -stand_call_conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} -dcov ${params.gatk_downsample} --output_mode ${params.gatk_ug_out_mode} ${defaultbasequalities}
+    gatk3 -Xmx${task.memory.toGiga()}g -T RealignerTargetCreator -R ${fasta} -I ${bam} -nt ${task.cpus} -o ${samplename}.intervals ${defaultbasequalities}
+    gatk3 -Xmx${task.memory.toGiga()}g -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${samplenane}.intervals -o ${samplename}.realign.bam ${defaultbasequalities}
+    gatk3 -Xmx${task.memory.toGiga()}g -T UnifiedGenotyper -R ${fasta} -I ${samplename}.realign.bam -o ${samplename}.unifiedgenotyper.vcf -nt ${task.cpus} --dbsnp ${params.gatk_dbsnp} --genotype_likelihoods_model ${params.gatk_ug_genotype_model} -stand_call_conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} -dcov ${params.gatk_downsample} --output_mode ${params.gatk_ug_out_mode} ${defaultbasequalities}
     
     $keep_realign
     
@@ -2398,13 +2398,13 @@ process genotyping_hc {
   script:
   if (!params.gatk_dbsnp)
     """
-    gatk HaplotypeCaller -R ${fasta} -I ${bam} -O ${samplename}.haplotypecaller.vcf -stand-call-conf ${params.gatk_call_conf} --sample-ploidy ${params.gatk_ploidy} --output-mode ${params.gatk_hc_out_mode} --emit-ref-confidence ${params.gatk_hc_emitrefconf}
+    gatk HaplotypeCaller --java-options "-Xmx${task.memory.toGiga()}G" -R ${fasta} -I ${bam} -O ${samplename}.haplotypecaller.vcf -stand-call-conf ${params.gatk_call_conf} --sample-ploidy ${params.gatk_ploidy} --output-mode ${params.gatk_hc_out_mode} --emit-ref-confidence ${params.gatk_hc_emitrefconf}
     bgzip -@ ${task.cpus} ${samplename}.haplotypecaller.vcf
     """
 
   else if (params.gatk_dbsnp)
     """
-    gatk HaplotypeCaller -R ${fasta} -I ${bam} -O ${samplename}.haplotypecaller.vcf --dbsnp ${params.gatk_dbsnp} -stand-call-conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} --output_mode ${params.gatk_hc_out_mode} --emit-ref-confidence ${params.gatk_hc_emitrefconf}
+    gatk HaplotypeCaller --java-options "-Xmx${task.memory.toGiga()}G" -R ${fasta} -I ${bam} -O ${samplename}.haplotypecaller.vcf --dbsnp ${params.gatk_dbsnp} -stand-call-conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} --output_mode ${params.gatk_hc_out_mode} --emit-ref-confidence ${params.gatk_hc_emitrefconf}
     bgzip -@  ${task.cpus} ${samplename}.haplotypecaller.vcf
     """
 }
@@ -2627,7 +2627,7 @@ process vcf2genome {
 if (!params.additional_vcf_files) {
     ch_vcfs_for_multivcfanalyzer = ch_ug_for_multivcfanalyzer.map{ it[-1] }.collect()
 } else {
-    ch_vcfs_for_multivcfanalyzer = ch_ug_for_multivcfanalyzer.map{ it [-1] }.collect().mix(ch_extravcfs_for_multivcfanalyzer)
+    ch_vcfs_for_multivcfanalyzer = ch_ug_for_multivcfanalyzer.map{ it[-1] }.mix(ch_extravcfs_for_multivcfanalyzer).collect().dump(tag: "postmix")
 }
 
 process multivcfanalyzer {