From 5efaf84ae0450406c060f6a591fc4278c6151d9a Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 21 May 2024 14:49:38 -0600 Subject: [PATCH 1/6] Update nextflow.config to 3.14.240521 --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 135daaa..51a09c1 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 = 'v3.13.20240514' + version = 'v3.14.240521' defaultBranch = 'master' recurseSubmodules = false description = 'Reference-based consensus creation' From 1020738138248c0692b5d9cbf58ac8187ec1669d Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 21 May 2024 14:50:14 -0600 Subject: [PATCH 2/6] Remove typo --- modules/artic.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/artic.nf b/modules/artic.nf index 66862b6..22b62d3 100644 --- a/modules/artic.nf +++ b/modules/artic.nf @@ -26,7 +26,7 @@ process artic { path "versions.yml", emit: versions shell: - def args = task.ext.args ?: "${params.artic_options}}" + def args = task.ext.args ?: "${params.artic_options}" def prefix = task.ext.prefix ?: "${sample}" """ mkdir -p artic consensus schema/cecret/V1 logs/${task.process} From a4cf00035aa470dd6bfce198f13a37af8d8cfd3d Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 21 May 2024 14:52:07 -0600 Subject: [PATCH 3/6] Fixed typo --- modules/minimap2.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/minimap2.nf b/modules/minimap2.nf index 024c12b..259c904 100644 --- a/modules/minimap2.nf +++ b/modules/minimap2.nf @@ -24,7 +24,7 @@ process minimap2 { path "versions.yml", emit: versions shell: - def args = task.ext.args ?: "${params.minimap2_options}}" + def args = task.ext.args ?: "${params.minimap2_options}" def fastq = reads.join(" ") def prefix = task.ext.prefix ?: "${sample}" """ From f62771a65132bf50d41a6c10d6d6d71c235f6aec Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 21 May 2024 14:53:43 -0600 Subject: [PATCH 4/6] Update freyja to 1.5.0-05_17_2024-01-06-2024-05-21 --- modules/freyja.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/freyja.nf b/modules/freyja.nf index 9c29998..4b33a8d 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:1.5.0-05_11_2024-01-10-2024-05-14' + container 'staphb/freyja:1.5.0-05_17_2024-01-06-2024-05-21' //#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:1.5.0-05_11_2024-01-10-2024-05-14' + container 'staphb/freyja:1.5.0-05_17_2024-01-06-2024-05-21' //#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:1.5.0-05_11_2024-01-10-2024-05-14' + container 'staphb/freyja:1.5.0-05_17_2024-01-06-2024-05-21' //#UPHLICA maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} From 4b53d3c22494398d53f03aceaa26608d29b8825e Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 21 May 2024 14:54:25 -0600 Subject: [PATCH 5/6] Update nextclade to 3.5.0 --- modules/nextclade.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nextclade.nf b/modules/nextclade.nf index eabf563..465a8b5 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:3.4.0' + container 'nextstrain/nextclade:3.5.0' //#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:3.4.0' + container 'nextstrain/nextclade:3.5.0' //#UPHLICA maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} From 78c165c528a3f678ca250817424237e926fafb8f Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 21 May 2024 14:55:04 -0600 Subject: [PATCH 6/6] Update iqtree2 to 2.3.1 --- modules/iqtree2.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/iqtree2.nf b/modules/iqtree2.nf index e3f3dff..4d29ef0 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 path: 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' //#UPHLICA maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}