From 2f0a11225548f53e1acb52d48d6d113843b5c730 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 23 Jul 2024 16:42:23 -0600 Subject: [PATCH 1/3] Update nextflow.config --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 4c127e45..01359648 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 = 'v3.15.24198' + version = 'v3.15.24205' defaultBranch = 'master' recurseSubmodules = false description = 'Reference-based consensus creation' From 9713a1c63efc38c3fd8a644fc8a253ed11c5be42 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 23 Jul 2024 16:43:18 -0600 Subject: [PATCH 2/3] Update nextclade to 3.8.2 --- modules/nextclade.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nextclade.nf b/modules/nextclade.nf index d4ea74a2..148dc8c6 100644 --- a/modules/nextclade.nf +++ b/modules/nextclade.nf @@ -2,7 +2,7 @@ process nextclade_dataset { tag "Downloading Dataset" label "process_medium" publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'nextstrain/nextclade:3.8.1' + container 'nextstrain/nextclade:3.8.2' //#UPHLICA maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} @@ -47,7 +47,7 @@ process nextclade { tag "Clade Determination" label "process_medium" publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'nextstrain/nextclade:3.8.1' + container 'nextstrain/nextclade:3.8.2' //#UPHLICA maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} From 59278ed075f160440e7172fa2f7fb95a0c1ba84c Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 23 Jul 2024 16:44:44 -0600 Subject: [PATCH 3/3] Update freyja to 1.5.1-07_02_2024-01-27-2024-07-23 --- modules/freyja.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/freyja.nf b/modules/freyja.nf index 14e3f3f9..2042eccd 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 path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/freyja:1.5.1-07_02_2024-01-27-2024-07-16' + container 'staphb/freyja:1.5.1-07_02_2024-01-27-2024-07-23' //#UPHLICA maxForks 10 //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge' @@ -53,7 +53,7 @@ process freyja_demix { label "process_medium" //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/freyja:1.5.1-07_02_2024-01-27-2024-07-16' + container 'staphb/freyja:1.5.1-07_02_2024-01-27-2024-07-23' //#UPHLICA maxForks 10 @@ -105,7 +105,7 @@ process freyja_aggregate { tag "Aggregating results from freyja" label "process_single" publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/freyja:1.5.1-07_02_2024-01-27-2024-07-16' + container 'staphb/freyja:1.5.1-07_02_2024-01-27-2024-07-23' //#UPHLICA maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}