From 0015788cc3c551630df1e52bb8be17c0cb5b3825 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 7 Sep 2023 14:08:20 +0200 Subject: [PATCH 1/4] Update to latest varlociraptor --- workflow/envs/varlociraptor.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/envs/varlociraptor.yaml b/workflow/envs/varlociraptor.yaml index 151fb266..e575e9a8 100644 --- a/workflow/envs/varlociraptor.yaml +++ b/workflow/envs/varlociraptor.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - varlociraptor =6.0 + - varlociraptor =8.3 From ccfd292c152f150e7b5f457d951565a3fd137077 Mon Sep 17 00:00:00 2001 From: Alexander Thomas <77535027+alethomas@users.noreply.github.com> Date: Thu, 21 Sep 2023 13:17:05 +0200 Subject: [PATCH 2/4] Update varlociraptor.yaml --- workflow/envs/varlociraptor.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/envs/varlociraptor.yaml b/workflow/envs/varlociraptor.yaml index e575e9a8..8501cab7 100644 --- a/workflow/envs/varlociraptor.yaml +++ b/workflow/envs/varlociraptor.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - varlociraptor =8.3 + - varlociraptor =8.4 From 581da5989d4a305e168db1d5b8841b6863ede434 Mon Sep 17 00:00:00 2001 From: Alexander Thomas <77535027+alethomas@users.noreply.github.com> Date: Tue, 24 Oct 2023 16:54:14 +0200 Subject: [PATCH 3/4] Update config.yaml --- config/config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/config/config.yaml b/config/config.yaml index afea4a94..898b305a 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -72,12 +72,12 @@ assembly: # assemblers used for shotgun sequencing with on Illumina technology shotgun: "megahit-std" # assemblers used for amplicon sequencing with on Illumina technology - amplicon: "metaspades" + amplicon: "megahit-std" oxford nanopore: # assemblers used for shotgun sequencing with on Oxford Nanopore technology shotgun: "megahit-std" # assemblers used for amplicon sequencing with on Oxford Nanopore technology - amplicon: "spades" + amplicon: "megahit-std" # Medaka models are named to indicate i) the pore type, ii) the sequencing device (MinION or PromethION), iii) the basecaller variant, and iv) the basecaller version # with the format: {pore}_{device}_{caller variant}_{caller version} # See https://github.com/nanoporetech/medaka#models for more information. @@ -86,7 +86,7 @@ assembly: # assemblers used for shotgun sequencing with on Ion Torrent technology shotgun: "megahit-std" # assemblers used for amplicon sequencing with on Torrent technology - amplicon: "spades" + amplicon: "megahit-std" # minimum posterior probability for a clonal variant to be included in the generated pseudo-assembly min-variant-prob: 0.95 From c50237f3f8ce8cdd45fde4f0f60b12815dc74909 Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Sat, 11 Nov 2023 15:17:34 +0100 Subject: [PATCH 4/4] trigger rerun