From 4e8089ee357a8bd06bcea13d8ec5515188671cbb Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 14 May 2024 11:25:38 -0600 Subject: [PATCH 1/5] Update to 4.2.240514 --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 3c7b256..20dacf7 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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' From 318c57c0c875f7c9bb4811a977bd453b0eda255b Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 14 May 2024 11:26:15 -0600 Subject: [PATCH 2/5] Update panaroo to 1.5.0 --- modules/local/panaroo.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/panaroo.nf b/modules/local/panaroo.nf index 04ca5a8..3c17fb0 100755 --- a/modules/local/panaroo.nf +++ b/modules/local/panaroo.nf @@ -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' From 9deb9f9e4d6fc1d2c0c4b9d87377d23f57246a64 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 14 May 2024 11:26:58 -0600 Subject: [PATCH 3/5] Update iqtree2 to 2.3.1 --- modules/local/iqtree2.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/iqtree2.nf b/modules/local/iqtree2.nf index d1ad8f3..8ae7366 100644 --- a/modules/local/iqtree2.nf +++ b/modules/local/iqtree2.nf @@ -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'} From 9ff61a419be8a7807906d5067b7b6364fb1b4703 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 14 May 2024 11:27:34 -0600 Subject: [PATCH 4/5] Update mlst to 2.23.0-2024-05-01 --- modules/local/mlst.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/mlst.nf b/modules/local/mlst.nf index 416ea86..6710565 100644 --- a/modules/local/mlst.nf +++ b/modules/local/mlst.nf @@ -2,7 +2,7 @@ process mlst { tag "${meta.id}" label "process_medium" publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/mlst:2.23.0-2024-04-01' + container 'staphb/mlst:2.23.0-2024-05-01' maxForks 10 errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} time '10m' From d28847e6d4c1f5eaf6c931ebbc67c8fc857352c4 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 14 May 2024 11:28:32 -0600 Subject: [PATCH 5/5] Update amrfinderplus to 3.12.8-2024-05-02.2 --- modules/local/amrfinderplus.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/amrfinderplus.nf b/modules/local/amrfinderplus.nf index 320dc2a..2d21f9a 100644 --- a/modules/local/amrfinderplus.nf +++ b/modules/local/amrfinderplus.nf @@ -2,7 +2,7 @@ process amrfinderplus { tag "${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'