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Update 20240514 #198

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Update 20240514 #198

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4e8089e
Update to 4.2.240514
erinyoung May 14, 2024
318c57c
Update panaroo to 1.5.0
erinyoung May 14, 2024
9deb9f9
Update iqtree2 to 2.3.1
erinyoung May 14, 2024
9ff61a4
Update mlst to 2.23.0-2024-05-01
erinyoung May 14, 2024
d28847e
Update amrfinderplus to 3.12.8-2024-05-02.2
erinyoung May 14, 2024
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2 changes: 1 addition & 1 deletion modules/local/amrfinderplus.nf
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Expand Up @@ -2,7 +2,7 @@ process amrfinderplus {
tag "${meta.id}"
label "process_high"
publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/ncbi-amrfinderplus:3.12.8-2024-01-31.1_2'
container 'staphb/ncbi-amrfinderplus:3.12.8-2024-05-02.2'
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '30m'

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2 changes: 1 addition & 1 deletion modules/local/iqtree2.nf
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Expand Up @@ -2,7 +2,7 @@ process iqtree2 {
tag "Phylogenetic analysis"
label "process_high"
publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/iqtree2:2.2.2.7'
container 'staphb/iqtree2:2.3.1'
time '24h'
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}

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2 changes: 1 addition & 1 deletion modules/local/mlst.nf
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Expand Up @@ -2,7 +2,7 @@ process mlst {
tag "${meta.id}"
label "process_medium"
publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/mlst:2.23.0-2024-04-01'
container 'staphb/mlst:2.23.0-2024-05-01'
maxForks 10
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '10m'
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2 changes: 1 addition & 1 deletion modules/local/panaroo.nf
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Expand Up @@ -2,7 +2,7 @@ process panaroo {
tag "Core Genome Alignment"
label "process_high"
publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/panaroo:1.3.4'
container 'staphb/panaroo:1.5.0'
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '10h'

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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -3,7 +3,7 @@ manifest {
author = 'Erin Young'
homePage = 'https://github.com/UPHL-BioNGS/Grandeur'
mainScript = 'main.nf'
version = '4.2.20240425'
version = '4.2.240514'
defaultBranch = 'main'
description = 'Grandeur is short-read de novo assembly pipeline with serotyping.'
nextflowVersion = '!>=22.10.1'
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