Merge pull request #11 from TRON-Bioinformatics/snpeff-memory

parametrise SnpEff memory

Author: priesgo

README.md

@@ -80,6 +80,7 @@ Optional input:
     * --snpeff_organism: the SnpEff organism name (eg: hg19, hg38, GRCh37.75, GRCh38.99)
     * --snpeff_datadir: the SnpEff data folder where the reference genomes were previously downloaded. Required if --snpeff_organism is provided
     * --snpeff_args: additional SnpEff arguments
+    * --snpeff_memory: for some samples SnpEff may require to use more memory (default: 3g)
     * --mapping_quality: VAFator minimum mapping quality (default: 0)
     * --base_call_quality: VAFator minimum base call quality (default: 0)
 

modules/05_variant_annotation.nf

@@ -1,3 +1,4 @@
+params.snpeff_memory = "3g"
 params.memory = "3g"
 params.cpus = 1
 params.output = "."
@@ -8,8 +9,9 @@ params.snpeff_args = ""
 
 process VARIANT_ANNOTATION_SNPEFF {
     cpus params.cpus
-    memory params.memory
+    memory params.snpeff_memory
     publishDir "${params.output}/${name}", mode: "copy"
+    tag "${name}"
 
     conda (params.enable_conda ? "bioconda::snpeff=5.0" : null)
 
@@ -22,14 +24,17 @@ process VARIANT_ANNOTATION_SNPEFF {
     script:
     datadir_arg = params.snpeff_datadir ? "-dataDir ${params.snpeff_datadir}" : ""
     """
-    snpEff eff ${datadir_arg} ${params.snpeff_args} -nodownload ${params.snpeff_organism} ${vcf} > ${name}.annotated.vcf
+    snpEff -Xmx${params.snpeff_memory} eff \
+    ${datadir_arg} ${params.snpeff_args} \
+    -nodownload ${params.snpeff_organism} ${vcf} > ${name}.annotated.vcf
     """
 }
 
 process VARIANT_ANNOTATION_BCFTOOLS {
     cpus params.cpus
     memory params.memory
     publishDir "${params.output}/${name}", mode: "copy"
+    tag "${name}"
 
     conda (params.enable_conda ? "conda-forge::libgcc-ng=10.3.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
 

nextflow.config

@@ -27,7 +27,7 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
-VERSION = '2.4.0'
+VERSION = '2.4.1'
 
 manifest {
   name = 'TRON-Bioinformatics/tronflow-vcf-postprocessing'
@@ -84,6 +84,7 @@ Optional input:
     * --snpeff_organism: the SnpEff organism name (eg: hg19, hg38, GRCh37.75, GRCh38.99)
     * --snpeff_datadir: the SnpEff data folder where the reference genomes were previously downloaded. Required if --snpeff_organism is provided
     * --snpeff_args: additional SnpEff arguments
+    * --snpeff_memory: for some samples SnpEff may require to use more memory (default: 3g)
     * --mapping_quality: VAFator minimum mapping quality (default: 0)
     * --base_call_quality: VAFator minimum base call quality (default: 0)