From 6938004635efd0a9c952d610acda9cf1eb927480 Mon Sep 17 00:00:00 2001
From: Valentina Galata <valentina.galata@uni.lu>
Date: Tue, 12 Jan 2021 08:09:29 +0100
Subject: [PATCH] config: updated rumen
---
config/rumen/config.yaml | 7 +++----
config/rumen/slurm.yaml | 40 ++++++++++++++++++++--------------------
2 files changed, 23 insertions(+), 24 deletions(-)
diff --git a/config/rumen/config.yaml b/config/rumen/config.yaml
index fe97bb6..5d796ae 100644
--- a/config/rumen/config.yaml
+++ b/config/rumen/config.yaml
@@ -2,10 +2,9 @@
# STEPS
# Steps to be done
-# steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
-steps: ["preprocessing", "assembly", "mapping"]
-steps_annotation: ["rgi", "plasflow", "minced", "barrnap", "kegg"] # prodigal is run in any case
-steps_analysis: ["quast", "mash", "mashmap", "fastani", "mummer", "cdhit", "diamond", "cov"]
+steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
+steps_annotation: ["rgi", "plasflow", "minced", "barrnap"] # prodigal is run in any case; excluded: kegg
+steps_analysis: ["quast", "mash", "mashmap", "fastani", "cdhit", "diamond", "cov"] # excluded: mummer
steps_taxonomy: ["kraken2", "kaiju"]
############################################################
diff --git a/config/rumen/slurm.yaml b/config/rumen/slurm.yaml
index 4f4dcb0..9f0536d 100644
--- a/config/rumen/slurm.yaml
+++ b/config/rumen/slurm.yaml
@@ -79,11 +79,11 @@ mapping_bwa_idx_asm:
mapping_bwa_mem_asm_sr:
time: "00-02:00:00"
- partition: "batch"
+ partition: "bigmem"
mapping_bwa_mem_asm_lr:
time: "00-08:00:00"
- partition: "batch"
+ partition: "bigmem"
mapping_bwa_mem_asm_hy:
time: "00-02:00:00"
@@ -99,72 +99,72 @@ annotation_rgi:
partition: "batch"
annotation_minced:
- time: "00-00:05:00"
+ time: "00-00:20:00"
partition: "batch"
annotation_plasflow:
- time: "00-00:10:00"
+ time: "00-00:30:00"
partition: "bigmem"
annotation_barrnap:
- time: "00-00:10:00"
+ time: "00-00:20:00"
partition: "batch"
annotation_hmm_kegg:
time: "00-08:00:00"
- partition: "batch"
+ partition: "bigmem"
# Analysis
analysis_quast:
- time: "00-00:05:00"
+ time: "00-00:10:00"
partition: "batch"
analysis_mash_sketch_sr:
- time: "00-00:15:00"
+ time: "00-00:40:00"
partition: "batch"
analysis_mash_sketch_lr:
- time: "00-00:15:00"
+ time: "00-00:40:00"
partition: "batch"
analysis_mash_reads:
- time: "00-00:05:00"
+ time: "00-00:10:00"
partition: "batch"
analysis_mash_sketch_asm:
- time: "00-00:05:00"
+ time: "00-00:10:00"
partition: "batch"
analysis_mash_asm:
- time: "00-00:05:00"
+ time: "00-00:10:00"
partition: "batch"
analysis_mashmap_one2one:
- time: "00-00:30:00"
+ time: "00-01:00:00"
partition: "batch"
analysis_fastani_one2one:
- time: "00-00:20:00"
+ time: "00-01:00:00"
partition: "batch"
analysis_mummer_dnadiff:
- time: "00-01:00:00"
- partition: "batch"
+ time: "00-02:00:00"
+ partition: "bigmem"
analysis_cdhit:
- time: "00-00:05:00"
+ time: "00-01:00:00"
partition: "batch"
analysis_diamond:
- time: "00-00:10:00"
+ time: "00-01:00:00"
partition: "batch"
analysis_diamond_db:
- time: "00-02:00:00"
+ time: "00-06:00:00"
partition: "batch"
analysis_genomecov_pergene:
- time: "00-02:00:00"
+ time: "00-12:00:00"
partition: "batch"
analysis_genomecov_segmentation:
--
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