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Update 20231031 #248

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merged 4 commits into from
Oct 31, 2023
Merged

Update 20231031 #248

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82bcd41
Update freyja to 1.4.7-2023-10-31
erinyoung Oct 31, 2023
7c214b9
Update version to 3.8.20231031
erinyoung Oct 31, 2023
187c266
log files from ivar trim std err
erinyoung Oct 31, 2023
844c6f7
Update pangolin to version 4.3.1-pdata-1.23.1
erinyoung Oct 31, 2023
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4 changes: 2 additions & 2 deletions modules/freyja.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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'
Expand Down Expand Up @@ -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'}
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2 changes: 1 addition & 1 deletion modules/ivar.nf
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Expand Up @@ -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 $log
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2 changes: 1 addition & 1 deletion modules/pangolin.nf
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Expand Up @@ -2,7 +2,7 @@ process pangolin {
tag "SARS-CoV-2 lineage Determination"
label "process_medium"
publishDir "${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'}
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -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'
Expand Down