From b8b0a67b16d2d78232bcd07ce4a9e20fd7610b23 Mon Sep 17 00:00:00 2001 From: Erin Young Date: Thu, 13 Apr 2023 13:29:51 -0600 Subject: [PATCH] updated container --- modules/amrfinderplus.nf | 2 +- modules/datasets.nf | 4 ++-- modules/fastqc.nf | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/amrfinderplus.nf b/modules/amrfinderplus.nf index 3ea6a59..ed2853f 100644 --- a/modules/amrfinderplus.nf +++ b/modules/amrfinderplus.nf @@ -2,7 +2,7 @@ process amrfinderplus { tag "${sample}" label "medcpus" publishDir params.outdir, mode: 'copy' - container 'staphb/ncbi-amrfinderplus:3.11.4-2023-02-23.1' + container 'staphb/ncbi-amrfinderplus:3.11.8-2023-02-23.1' maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} //#UPHLICA cpus 7 diff --git a/modules/datasets.nf b/modules/datasets.nf index 5dab680..eff1b5f 100644 --- a/modules/datasets.nf +++ b/modules/datasets.nf @@ -1,7 +1,7 @@ process datasets_summary { tag "${taxon}" publishDir params.outdir, mode: 'copy' - container 'staphb/ncbi-datasets:14.13.2' + container 'staphb/ncbi-datasets:14.20.0' maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-medium' @@ -43,7 +43,7 @@ process datasets_download { // because there's no way to specify threads label "medcpus" publishDir params.outdir, mode: 'copy' - container 'staphb/ncbi-datasets:14.7.0' + container 'staphb/ncbi-datasets:14.20.0' maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-medium' diff --git a/modules/fastqc.nf b/modules/fastqc.nf index 3bdc912..52f8f50 100644 --- a/modules/fastqc.nf +++ b/modules/fastqc.nf @@ -1,7 +1,7 @@ process fastqc { tag "${sample}" publishDir params.outdir, mode: 'copy' - container 'staphb/fastqc:0.11.9' + container 'staphb/fastqc:0.12.1' maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-medium'