From 03edf0fc81d0e6249342fad04c3fa757caf70897 Mon Sep 17 00:00:00 2001 From: Ubuntu Date: Tue, 24 Oct 2023 08:54:59 +0000 Subject: [PATCH 1/3] update gffults & qc --- workflow/envs/gffutils.yaml | 2 +- workflow/rules/qc.smk | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/workflow/envs/gffutils.yaml b/workflow/envs/gffutils.yaml index 2959827..931f26f 100644 --- a/workflow/envs/gffutils.yaml +++ b/workflow/envs/gffutils.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - gffutils =0.11 + - gffutils =0.12 diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk index 02a60a5..aaab7c0 100644 --- a/workflow/rules/qc.smk +++ b/workflow/rules/qc.smk @@ -193,4 +193,4 @@ rule multiqc: log: "logs/multiqc.log", wrapper: - "v1.21.4/bio/multiqc" + "v2.7.0/bio/multiqc" From 8faf6c8da88bddfc7b23c2e2c6db92f3d7f17b1e Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Tue, 24 Oct 2023 11:34:29 +0200 Subject: [PATCH 2/3] fix indentationg of rule multiqc wrapper version spec line --- workflow/rules/qc.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk index aaab7c0..da62289 100644 --- a/workflow/rules/qc.smk +++ b/workflow/rules/qc.smk @@ -193,4 +193,4 @@ rule multiqc: log: "logs/multiqc.log", wrapper: - "v2.7.0/bio/multiqc" + "v2.7.0/bio/multiqc" From 4bb1f77e0242d027b7663697f3c4a7568e431c28 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Tue, 24 Oct 2023 16:00:31 +0200 Subject: [PATCH 3/3] fix: biomart race conditions should be fixed in newer versions via https://github.com/grimbough/biomaRt/commit/94a1f92bb10f18c442e6320d0c51f2a499817762 --- workflow/envs/biomart.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflow/envs/biomart.yaml b/workflow/envs/biomart.yaml index 16a0027..04342c7 100644 --- a/workflow/envs/biomart.yaml +++ b/workflow/envs/biomart.yaml @@ -3,5 +3,5 @@ channels: - bioconda - nodefaults dependencies: - - bioconductor-biomart =2.54 - - r-tidyverse =1.3 + - bioconductor-biomart =2.56 + - r-tidyverse =2.0