diff --git a/modules/freyja.nf b/modules/freyja.nf index cb48861..a67f89b 100644 --- a/modules/freyja.nf +++ b/modules/freyja.nf @@ -3,7 +3,7 @@ process freyja { label "process_medium" errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} publishDir "${params.outdir}", mode: 'copy' - container 'quay.io/uphl/freyja:1.4.7-2023-10-24' + container 'quay.io/uphl/freyja:1.4.7-2023-10-31' //#UPHLICA maxForks 10 //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge' @@ -57,7 +57,7 @@ process freyja_aggregate { tag "Aggregating results from freyja" label "process_single" publishDir "${params.outdir}", mode: 'copy' - container 'quay.io/uphl/freyja:1.4.7-2023-10-24' + container 'quay.io/uphl/freyja:1.4.7-2023-10-31' //#UPHLICA maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} diff --git a/modules/ivar.nf b/modules/ivar.nf index e06257d..1955806 100644 --- a/modules/ivar.nf +++ b/modules/ivar.nf @@ -138,7 +138,7 @@ process ivar_trim { # trimming the reads ivar trim !{params.ivar_trim_options} -e -i !{bam} -b !{primer_bed} -p ivar_trim/!{sample}.primertrim | tee -a $log - if [ -S "$log" ] ; then grep "Found" -A 10000 $log | grep -A 10000 "primers in BED file" > ivar_trim/!{sample}_ivar.log ; else touch ivar_trim/!{sample}_ivar.log ; fi + if [ -S "$log" ] ; then grep "Found" -A 10000 $log | grep -A 10000 "primers in BED file" 2> ivar_trim/!{sample}_ivar.log ; else touch ivar_trim/!{sample}_ivar.log ; fi # sorting and indexing the trimmed bams samtools sort ivar_trim/!{sample}.primertrim.bam -o ivar_trim/!{sample}.primertrim.sorted.bam | tee -a $log diff --git a/modules/pangolin.nf b/modules/pangolin.nf index 34633f2..72b778b 100644 --- a/modules/pangolin.nf +++ b/modules/pangolin.nf @@ -2,7 +2,7 @@ process pangolin { tag "SARS-CoV-2 lineage Determination" label "process_medium" publishDir "${params.outdir}", mode: 'copy' - container 'staphb/pangolin:4.3.1-pdata-1.22' + container 'staphb/pangolin:4.3.1-pdata-1.23.1' //#UPHLICA maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} diff --git a/nextflow.config b/nextflow.config index 7a272c9..795d98d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -5,7 +5,7 @@ manifest { name = 'Cecret' author = 'Erin Young' homePage = 'https://github.com/UPHL-BioNGS/Cecret' - version = 'v3.8.20231024' + version = 'v3.8.20231031' defaultBranch = 'master' recurseSubmodules = false description = 'Reference-based consensus creation'