From f419b95c646d387232fb586b399895abb1a5df07 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 6 Feb 2024 10:42:36 -0700 Subject: [PATCH 1/4] Update freyja to 1.4.8-2024-02-06 --- modules/freyja.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/freyja.nf b/modules/freyja.nf index 26672e20..ec81739a 100644 --- a/modules/freyja.nf +++ b/modules/freyja.nf @@ -3,7 +3,7 @@ process freyja_variants { label "process_medium" //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} publishDir "${params.outdir}", mode: 'copy' - container 'quay.io/uphl/freyja:1.4.8-2024-01-30' + container 'quay.io/uphl/freyja:1.4.8-2024-02-06' //#UPHLICA maxForks 10 @@ -45,7 +45,7 @@ process freyja_demix { label "process_medium" //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} publishDir "${params.outdir}", mode: 'copy' - container 'quay.io/uphl/freyja:1.4.8-2024-01-30' + container 'quay.io/uphl/freyja:1.4.8-2024-02-06' //#UPHLICA maxForks 10 @@ -87,7 +87,7 @@ process freyja_boot { label "process_medium" //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} publishDir "${params.outdir}", mode: 'copy' - container 'quay.io/uphl/freyja:1.4.8-2024-01-30' + container 'quay.io/uphl/freyja:1.4.8-2024-02-06' //#UPHLICA maxForks 10 //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge' @@ -126,7 +126,7 @@ process freyja_aggregate { tag "Aggregating results from freyja" label "process_single" publishDir "${params.outdir}", mode: 'copy' - container 'quay.io/uphl/freyja:1.4.8-2024-01-30' + container 'quay.io/uphl/freyja:1.4.8-2024-02-06' //#UPHLICA maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} From d973a1308d1646db50b356cdd3fbbf1c1d0eea5e Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 6 Feb 2024 10:44:25 -0700 Subject: [PATCH 2/4] Update iqtree2 to 2.2.2.7 --- modules/iqtree2.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/iqtree2.nf b/modules/iqtree2.nf index a080668c..ccbe20b8 100644 --- a/modules/iqtree2.nf +++ b/modules/iqtree2.nf @@ -2,7 +2,7 @@ process iqtree2 { tag "Creating phylogenetic tree with iqtree" label "process_high" publishDir "${params.outdir}", mode: 'copy' - container 'staphb/iqtree2:2.2.2.6' + container 'staphb/iqtree2:2.2.2.7' //#UPHLICA maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} From 2c601a669f31738c908ad7e5c39c91b3b7aed521 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 6 Feb 2024 10:44:56 -0700 Subject: [PATCH 3/4] Update nextflow.config to 3.11.20240206 --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 7ee8cc9e..fde09656 100644 --- a/nextflow.config +++ b/nextflow.config @@ -5,7 +5,7 @@ manifest { name = 'Cecret' author = 'Erin Young' homePage = 'https://github.com/UPHL-BioNGS/Cecret' - version = 'v3.11.20240130' + version = 'v3.11.20240206' defaultBranch = 'master' recurseSubmodules = false description = 'Reference-based consensus creation' From e2a076afb28be7ba2f66d8384f1a22491c20d466 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 6 Feb 2024 10:45:55 -0700 Subject: [PATCH 4/4] Update nextclade to 3.1.0 --- modules/nextclade.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nextclade.nf b/modules/nextclade.nf index 7018aaa7..16f9b2e4 100644 --- a/modules/nextclade.nf +++ b/modules/nextclade.nf @@ -2,7 +2,7 @@ process nextclade_dataset { tag "Downloading NextClade Dataset" label "process_medium" publishDir "${params.outdir}", mode: 'copy' - container 'nextstrain/nextclade:3.0.1' + container 'nextstrain/nextclade:3.1.0' //#UPHLICA maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} @@ -38,7 +38,7 @@ process nextclade { tag "Clade Determination" label "process_medium" publishDir "${params.outdir}", mode: 'copy' - container 'nextstrain/nextclade:3.0.1' + container 'nextstrain/nextclade:3.1.0' //#UPHLICA maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}