From 0de4620243f4c3a5aca2d781c6b98f7bba40ca9d Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 5 Nov 2024 15:20:23 -0700 Subject: [PATCH 1/8] Update to 4.5.24310 --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 991d523..1a984fd 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 = '4.5.24276' + version = '4.5.24310' defaultBranch = 'main' description = 'Grandeur is short-read de novo assembly pipeline with serotyping.' nextflowVersion = '!>=22.10.1' From c134a88330d4459282294257af265f3633cc189f Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 5 Nov 2024 15:21:28 -0700 Subject: [PATCH 2/8] Update mlst to 2.23.0-2024-11-01 --- 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 891ce19..ef6735c 100644 --- a/modules/local/mlst.nf +++ b/modules/local/mlst.nf @@ -2,7 +2,7 @@ process mlst { tag "${meta.id}" label "process_medium" publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/mlst:2.23.0-2024-10-01' + container 'staphb/mlst:2.23.0-2024-11-01' maxForks 10 errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} time '10m' From c368f0dc1a64016751445d81bb91479a04df7e5e Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 5 Nov 2024 15:22:06 -0700 Subject: [PATCH 3/8] Update blast to 2.16.0 --- modules/local/blast.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/blast.nf b/modules/local/blast.nf index 5fa73a9..79bb282 100644 --- a/modules/local/blast.nf +++ b/modules/local/blast.nf @@ -2,7 +2,7 @@ process blastn { tag "${meta.id}" label "process_medium" publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/blast:2.15.0' + container 'staphb/blast:2.16.0' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} time '2h' From 16275401981ea8477d9f9d8783feeceea6ba7383 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 5 Nov 2024 15:22:25 -0700 Subject: [PATCH 4/8] Update elgato to 1.20.1 --- modules/local/elgato.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/elgato.nf b/modules/local/elgato.nf index d5e33a8..fff910e 100755 --- a/modules/local/elgato.nf +++ b/modules/local/elgato.nf @@ -2,7 +2,7 @@ process elgato { tag "${meta.id}" label "process_medium" publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/elgato:1.19.0' + container 'staphb/elgato:1.20.1' time '10m' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} From 5fd8b0d44da8d21cfde19d80953f8fa6de3515c1 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 5 Nov 2024 15:22:52 -0700 Subject: [PATCH 5/8] Update iqtree2 to 2.3.6 --- modules/local/iqtree2.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/iqtree2.nf b/modules/local/iqtree2.nf index 8ae7366..4698a85 100644 --- a/modules/local/iqtree2.nf +++ b/modules/local/iqtree2.nf @@ -2,7 +2,7 @@ process iqtree2 { tag "Phylogenetic analysis" label "process_high" publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/iqtree2:2.3.1' + container 'staphb/iqtree2:2.3.6' time '24h' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} From 26de9c699b3850356ad6f53da35c2c5398d864db Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 5 Nov 2024 15:24:02 -0700 Subject: [PATCH 6/8] Update datasets to 16.30.0 --- modules/local/datasets.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/datasets.nf b/modules/local/datasets.nf index 4ef6a81..ce0738b 100644 --- a/modules/local/datasets.nf +++ b/modules/local/datasets.nf @@ -2,7 +2,7 @@ process datasets_summary { tag "${taxon}" label "process_single" publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/ncbi-datasets:16.22.1' + container 'staphb/ncbi-datasets:16.30.0' time '1h' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore' } @@ -52,7 +52,7 @@ process datasets_download { // because there's no way to specify threads label "process_medium" publishDir path: "${params.outdir}", mode: 'copy', pattern: "logs/*/*log" - container 'staphb/ncbi-datasets:16.22.1' + container 'staphb/ncbi-datasets:16.30.0' time '5h' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} From 8eae175bb2778dd48057b01bdd8e4063b40747cc Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 5 Nov 2024 15:26:24 -0700 Subject: [PATCH 7/8] Update pbptyper to 2.0.0 --- modules/local/pbptyper.nf | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/modules/local/pbptyper.nf b/modules/local/pbptyper.nf index 9cb85d5..75a491e 100644 --- a/modules/local/pbptyper.nf +++ b/modules/local/pbptyper.nf @@ -3,7 +3,7 @@ process pbptyper { label "process_medium" stageInMode "copy" publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/pbptyper:1.0.4' + container 'staphb/pbptyper:2.0.0' time '1h' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} @@ -27,7 +27,9 @@ process pbptyper { log_file=logs/${task.process}/${prefix}.${workflow.sessionId}.log pbptyper ${args} \ - --assembly ${contigs} \ + --yaml data/pbptyper.yaml \ + --targets data/pbptyper.fasta \ + --input ${contigs} \ --prefix ${prefix} \ --outdir pbptyper \ | tee -a \$log_file @@ -37,4 +39,4 @@ process pbptyper { pbptyper: \$(echo \$(pbptyper --version 2>&1) | sed 's/^.*pbptyper, version //;' ) END_VERSIONS """ -} \ No newline at end of file +} From d910aa465d71594851d02d651ff6e252797ff291 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 5 Nov 2024 15:42:33 -0700 Subject: [PATCH 8/8] Update pbptyper.nf --- modules/local/pbptyper.nf | 2 -- 1 file changed, 2 deletions(-) diff --git a/modules/local/pbptyper.nf b/modules/local/pbptyper.nf index 75a491e..85a0e3c 100644 --- a/modules/local/pbptyper.nf +++ b/modules/local/pbptyper.nf @@ -27,8 +27,6 @@ process pbptyper { log_file=logs/${task.process}/${prefix}.${workflow.sessionId}.log pbptyper ${args} \ - --yaml data/pbptyper.yaml \ - --targets data/pbptyper.fasta \ --input ${contigs} \ --prefix ${prefix} \ --outdir pbptyper \