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Update 20231205 #264

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merged 7 commits into from
Dec 5, 2023
Merged

Update 20231205 #264

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a8d2079
Update artic container to 1.2.4-1.11.2-2023-12-05 for medaka
erinyoung Dec 5, 2023
9d018b3
Update freyja to 1.4.7-2023-12-05
erinyoung Dec 5, 2023
3e27709
Update heatcluster to 0.4.13-2023-12-05
erinyoung Dec 5, 2023
b5543ba
Changed to staphb image
erinyoung Dec 5, 2023
8f60a6c
Update minimap2 to 2.26
erinyoung Dec 5, 2023
97f3362
Update pangolin to use version 4.3.1-pdata-1.23.1-1
erinyoung Dec 5, 2023
20dd922
Update nextflow.config to version 3.10.20231205
erinyoung Dec 5, 2023
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2 changes: 1 addition & 1 deletion modules/artic.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ process artic {
tag "${sample}"
label "process_high"
publishDir "${params.outdir}", mode: 'copy'
container 'quay.io/uphl/artic:1.2.4-1.11.1'
container 'quay.io/uphl/artic:1.2.4-1.11.2-2023-12-05'

//#UPHLICA maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
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8 changes: 4 additions & 4 deletions modules/freyja.nf
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Expand Up @@ -3,7 +3,7 @@ process freyja_variants {
label "process_medium"
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
publishDir "${params.outdir}", mode: 'copy'
container 'quay.io/uphl/freyja:1.4.7-2023-11-28'
container 'quay.io/uphl/freyja:1.4.7-2023-12-05'

//#UPHLICA maxForks 10
//#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
Expand Down Expand Up @@ -44,7 +44,7 @@ process freyja_demix {
label "process_medium"
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
publishDir "${params.outdir}", mode: 'copy'
container 'quay.io/uphl/freyja:1.4.7-2023-11-28'
container 'quay.io/uphl/freyja:1.4.7-2023-12-05'

//#UPHLICA maxForks 10
//#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
Expand Down Expand Up @@ -85,7 +85,7 @@ process freyja_boot {
label "process_medium"
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
publishDir "${params.outdir}", mode: 'copy'
container 'quay.io/uphl/freyja:1.4.7-2023-11-28'
container 'quay.io/uphl/freyja:1.4.7-2023-12-05'

//#UPHLICA maxForks 10
//#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
Expand Down Expand Up @@ -124,7 +124,7 @@ process freyja_aggregate {
tag "Aggregating results from freyja"
label "process_single"
publishDir "${params.outdir}", mode: 'copy'
container 'quay.io/uphl/freyja:1.4.7-2023-11-28'
container 'quay.io/uphl/freyja:1.4.7-2023-12-05'

//#UPHLICA maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
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4 changes: 2 additions & 2 deletions modules/heatcluster.nf
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@@ -1,7 +1,7 @@
process heatcluster {
tag "HeatCluster"
publishDir params.outdir, mode: 'copy'
container 'quay.io/uphl/heatcluster:0.4.12-2023-11-15'
container 'quay.io/uphl/heatcluster:0.4.13-2023-12-05'
maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
//#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-medium'
Expand Down Expand Up @@ -39,4 +39,4 @@ process heatcluster {

if [ -f "heatcluster/heatcluster.png" ] ; then cp heatcluster/heatcluster.png heatcluster/heatcluster_mqc.png ; fi
'''
}
}
2 changes: 1 addition & 1 deletion modules/minimap2.nf
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Expand Up @@ -2,7 +2,7 @@ process minimap2 {
tag "${sample}"
label "process_high"
publishDir path: "${params.outdir}", mode: 'copy', pattern: 'logs/*/*log'
container 'staphb/minimap2:2.25'
container 'staphb/minimap2:2.26'

//#UPHLICA maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
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6 changes: 3 additions & 3 deletions 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-1.23.1'
container 'staphb/pangolin:4.3.1-pdata-1.23.1-1'

//#UPHLICA maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
Expand All @@ -24,7 +24,7 @@ process pangolin {

shell:
'''
mkdir -p temp pangolin logs/!{task.process}
mkdir -p pangolin logs/!{task.process}
log=logs/!{task.process}/!{task.process}.!{workflow.sessionId}.log

date > $log
Expand All @@ -38,10 +38,10 @@ process pangolin {
pangolin !{params.pangolin_options} \
--threads !{task.cpus} \
--outdir pangolin \
--tempdir temp \
--verbose \
ultimate_fasta.fasta \
| tee -a $log

cp ultimate_fasta.fasta pangolin/combined.fasta
'''
}
2 changes: 1 addition & 1 deletion modules/phytreeviz.nf
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Expand Up @@ -2,7 +2,7 @@ process phytreeviz {
tag "Tree visualization"
label "maxcpus"
publishDir params.outdir, mode: 'copy'
container 'quay.io/uphl/phytreeviz:0.1.0-2023-11-15'
container 'staphb/phytreeviz:0.1.0'
maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
//#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
Expand Down
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 = 'v3.10.20231128'
version = 'v3.10.20231205'
defaultBranch = 'master'
recurseSubmodules = false
description = 'Reference-based consensus creation'
Expand Down