diff --git a/lib/Utils.groovy b/lib/Utils.groovy index 895f775..3acd2fd 100644 --- a/lib/Utils.groovy +++ b/lib/Utils.groovy @@ -140,7 +140,7 @@ class Utils { Illumina FASTQs directory : ${params.illumina_fastq_dir ?: ""} Sample ID lookup : ${params.sample_lookup ?: ""} Results directory : ${params.results} - Email Address(es) : ${params.email ?: ""} + Email Address(es) : ${params.email ?: ""} """ .stripIndent() diff --git a/modules/snpeff.nf b/modules/snpeff.nf index e615e43..0199121 100644 --- a/modules/snpeff.nf +++ b/modules/snpeff.nf @@ -50,7 +50,7 @@ process ANNOTATE_VCF { script: """ cp ${snpeff_config} local.config && \ - snpEff -Xmx1g \ + snpEff -Xmx3g \ -c local.config \ -dataDir genome/ \ -v ref_genome \ @@ -77,7 +77,7 @@ process EXTRACT_FIELDS { script: """ - SnpSift -Xmx1g extractFields \ + SnpSift -Xmx3g extractFields \ -s "," \ ${vcf} \ CHROM REF POS ALT AF AC DP GEN[0].REF_DP GEN[0].ALT_DP GEN[0].ALT_FREQ MQ ANN[0].GENE ANN[0].EFFECT ANN[0].HGVS_P ANN[0].CDS_POS ANN[0].AA_POS \